def example2():
from pyigrf.pyigrf import GetIGRF
from scipy import arange, arcsin, rad2deg
xlat = -11.95
xlon = 283.13
year = 2004.75
altlim = [90, 500.]
altstp = 10.
altbins = arange(altlim[0], altlim[1] + altstp, altstp)
for i in range(len(altbins)):
bn, be, bd, xl, icode = GetIGRF(xlat, xlon, altbins[i], year)
# Horizontal component
bh = (bn**2 + be**2)**.5
# Total component
ba = (bn**2 + be**2 + bd**2)**.5
# Dip angle
dip = rad2deg(arcsin(bd / ba))
# Declination angle
dec = rad2deg(arcsin(be / bh))
print(i, altbins[i], bn, be, bd, xl, icode)
print(bh, ba, dip, dec)
print('')
def get_stroke_angle(t, f, amp, u, v, k, phase=0.5 * PI):
"""
Stroke position function w/ J. Wang's shape parameter. The control input
u adds a asymmetric velicty to the stroke positon fuction, while the control
input v adds changes the mean stroke position.
Arguments:
t = array of time points (s)
f = flapping frequency (Hz)
amp = stroke amplitude
u = control input, scalar or array
v = control input, s
k = shape parameter near 0 => sine wave, near 1=> sawtooth
"""
f1 = f / (2 * u)
f2 = 1 / (2 / f - 1 / f1)
phi_A = amp / scipy.arcsin(k) * scipy.arcsin(
k * scipy.sin(2 * PI * f1 * scipy.fmod(t, 1 / f) + phase))
phi_B = amp / scipy.arcsin(k) * scipy.arcsin(
k * scipy.sin(2 * PI * f2 * (1 / (2 * f2) - 1 /
(2 * f1) + scipy.fmod(t, 1 / f)) + phase))
phi = phi_A * (scipy.fmod(t, 1 / f) < 1 /
(2 * f1)) + phi_B * (scipy.fmod(t, 1 / f) >= 1 /
(2 * f1)) + v
return phi
def dl_to_rphi_2d(d,l,degree=False,ro=1.,phio=0.):
"""
NAME:
dl_to_rphi_2d
PURPOSE:
convert Galactic longitude and distance to Galactocentric radius and azimuth
INPUT:
d - distance
l - Galactic longitude [rad/deg if degree]
KEYWORDS:
degree= (False): l is in degrees rather than rad
ro= (1) Galactocentric radius of the observer
phio= (0) Galactocentric azimuth of the observer [rad/deg if degree]
OUTPUT:
(R,phi); phi in degree if degree
HISTORY:
2012-01-04 - Written - Bovy (IAS)
"""
scalarOut, listOut= False, False
if isinstance(d,(int,float)):
d= sc.array([d])
scalarOut= True
elif isinstance(d,list):
d= sc.array(d)
listOut= True
if isinstance(l,(int,float)):
l= sc.array([l])
elif isinstance(l,list):
l= sc.array(l)
if degree:
l*= _DEGTORAD
R= sc.sqrt(ro**2.+d**2.-2.*d*ro*sc.cos(l))
phi= sc.arcsin(d/R*sc.sin(l))
indx= (ro/sc.cos(l) < d)*(sc.cos(l) > 0.)
phi[indx]= sc.pi-sc.arcsin(d[indx]/R[indx]*sc.sin(l[indx]))
if degree:
phi/= _DEGTORAD
phi+= phio
if scalarOut:
return (R[0],phi[0])
elif listOut:
return (list(R),list(phi))
else:
return (R,phi)
def rphi_to_dl_2d(R,phi,degree=False,ro=1.,phio=0.):
"""
NAME:
rphi_to_dl_2d
PURPOSE:
convert Galactocentric radius and azimuth to distance and Galactic longitude
INPUT:
R - Galactocentric radius
phi - Galactocentric azimuth [rad/deg if degree]
KEYWORDS:
degree= (False): phi is in degrees rather than rad
ro= (1) Galactocentric radius of the observer
phio= (0) Galactocentric azimuth of the observer [rad/deg if degree]
OUTPUT:
(d,l); phi in degree if degree
HISTORY:
2012-01-04 - Written - Bovy (IAS)
"""
scalarOut, listOut= False, False
if isinstance(R,(int,float)):
R= sc.array([R])
scalarOut= True
elif isinstance(R,list):
R= sc.array(R)
listOut= True
if isinstance(phi,(int,float)):
phi= sc.array([phi])
elif isinstance(phi,list):
phi= sc.array(phi)
phi-= phio
if degree:
phi*= _DEGTORAD
d= sc.sqrt(R**2.+ro**2.-2.*R*ro*sc.cos(phi))
l= sc.arcsin(R/d*sc.sin(phi))
indx= (ro/sc.cos(phi) < R)*(sc.cos(phi) > 0.)
l[indx]= sc.pi-sc.arcsin(R[indx]/d[indx]*sc.sin(phi[indx]))
if degree:
l/= _DEGTORAD
if scalarOut:
return (d[0],l[0])
elif listOut:
return (list(d),list(l))
else:
return (d,l)
def get_angle (sin_in, cos_in):
""" Just use arctan2 - much more efficient"""
if (sin_in >= 0.0 and cos_in >= 0.0): out = sc.arcsin(sin_in)
elif (sin_in >= 0.0 and cos_in < 0.0): out = ma.pi-sc.arcsin(sin_in)
elif (sin_in < 0.0 and cos_in < 0.0): out = ma.pi-sc.arcsin(sin_in)
elif (sin_in < 0.0 and cos_in >= 0.0): out = 2.0*ma.pi + sc.arcsin(sin_in)
else: out = float('nan')
return out
def euler_from_qarray(q,tol=0.499):
"""
Get array of euler angles from array of quaternions. Note, array of euler angles
will be in columns of [heading,attitude,bank].
Euler angle convention - similar to NASA standard airplane, but with y and z axes
swapped to conform with x3d. (in order of application)
1.0 rotation about y-axis
2.0 rotation about z-axis
3.0 rotation about x-axis
"""
qw = q[:,0]
qx = q[:,1]
qy = q[:,2]
qz = q[:,3]
head = scipy.zeros((q.shape[0],))
atti = scipy.zeros((q.shape[0],))
bank = scipy.zeros((q.shape[0],))
test = qx*qy - qz*qw # test for north of south pole
# Points not at north or south pole
mask0 = scipy.logical_and(test <= tol, test >= -tol)
qw_0 = qw[mask0]
qx_0 = qx[mask0]
qy_0 = qy[mask0]
qz_0 = qz[mask0]
head[mask0] = scipy.arctan2(2.0*qy_0*qw_0 - 2.0*qx_0*qz_0, 1.0 - 2.0*qy_0**2 - 2.0*qz_0**2)
atti[mask0] = scipy.arcsin(2.0*qx_0*qy_0 + 2.0*qz_0*qw_0)
bank[mask0] = scipy.arctan2(2.0*qx_0*qw_0 - 2.0*qy_0*qz_0, 1.0 - 2.0*qx_0**2 - 2.0*qz_0**2)
# Points at north pole
mask1 = test > tol
qw_1 = qw[mask1]
qx_1 = qx[mask1]
qy_1 = qy[mask1]
qz_1 = qz[mask1]
head[mask1] = 2.0*scipy.arctan2(qx_1,qw_1)
atti[mask1] = scipy.arcsin(2.0*qx_1*qy_1 + 2.0*qz_1*qw_1)
bank[mask1] = scipy.zeros((qw_1.shape[0],))
# Points at south pole
mask2 = test < -tol
qw_2 = qw[mask2]
qx_2 = qx[mask2]
qy_2 = qy[mask2]
qz_2 = qz[mask2]
head[mask2] = -2.0*scipy.arctan2(qx_2,qw_2)
atti[mask2] = scipy.arcsin(2.0*qx_2*qy_2 + 2.0*qz_2*qw_2)
bank[mask2] = scipy.zeros((qw_2.shape[0],))
euler_angs = scipy.zeros((q.shape[0],3))
euler_angs[:,0] = head
euler_angs[:,1] = atti
euler_angs[:,2] = bank
return euler_angs
def phase(theta_i, alpha, p, m):
'''输入的theta 是角度不是弧度'''
theta_i = np.array(theta_i)
theta_i = theta_i * pi / 180
if p != 0:
theta_i[theta_i > real(arcsin(m))] = None
# costheta_r = np.sqrt(1 - np.sin(theta_i/m)**2)
theta_r = real(arcsin(sin(theta_i) / m)) # 这里默认给出复数形式，取实数部分，
return 2 * alpha * (cos(theta_i) - p * m * cos(theta_r))
def matrixToEuler(m,order='Aerospace',inDegrees=True):
if order == 'Aerospace' or order == 'ZYX':
sp = -m[2,0]
if sp < (1-EPS):
if sp > (-1+EPS):
p = arcsin(sp)
r = arctan2(m[2,1],m[2,2])
y = arctan2(m[1,0],m[0,0])
else:
p = -pi/2.
r = 0
y = pi-arctan2(-m[0,1],m[0,2])
else:
p = pi/2.
y = arctan2(-m[0,1],m[0,2])
r = 0
if inDegrees:
return degrees((y,p,r))
else:
return (y,p,r)
elif order == 'BVH' or order == 'ZXY':
sx = m[2,1]
if sx < (1-EPS):
if sx > (-1+EPS):
x = arcsin(sx)
z = arctan2(-m[0,1],m[1,1])
y = arctan2(-m[2,0],m[2,2])
else:
x = -pi/2
y = 0
z = -arctan2(m[0,2],m[0,0])
else:
x = pi/2
y = 0
z = arctan2(m[0,2],m[0,0])
if inDegrees:
return degrees((z,x,y))
else:
return (z,x,y)
elif order == "ZXZ":
x = arccos(m[2,2])
z2 = arctan2(m[2,0],m[2,1])
z1 = arctan2(m[0,2],-m[1,2])
if inDegrees:
return degrees((z1,x,z2))
else:
return (z1,x,z2)
def haversine(point1, point2, lon1=None, lat1=None, lon2=None, lat2=None):
"""
Haversine function calculates distance (in miles) between two points in lat/long coordinates. See
https://gis.stackexchange.com/questions/279109/calculate-distance-between-a-coordinate-and-a-county-in-geopandas
:param point1: Shapely point. Long then lat.
:param point2: Shapely point. Long then lat.
:param lon1, lat1, lon2, lat2: Alternatively, supply the longitudes and lattitudes manually.
:return: Distance in miles.
"""
# Retrieve lat and long
if lon1 is None or lat1 is None:
lon1, lat1 = list(point1.coords[:][0][0:])
if lon2 is None or lat2 is None:
lon2, lat2 = list(point2.coords[:][0][0:])
# convert decimal degrees to radians
lon1, lat1, lon2, lat2 = map(scipy.radians, [lon1, lat1, lon2, lat2])
# haversine formula
dlon = lon2 - lon1
dlat = lat2 - lat1
a = scipy.sin(dlat / 2)**2 + scipy.cos(lat1) * scipy.cos(lat2) * scipy.sin(
dlon / 2)**2
c = 2 * scipy.arcsin(scipy.sqrt(a))
r = 3956 # Radius of earth in miles. Use 6371 for km
return c * r
def to_YPR(quaternion):
q0, q1, q2, q3 = quaternion
roll = sp.arctan2(2 * (q0 * q1 + q2 * q3), (q0**2 - q1**2 - q2**2 + q3**2))
pitch = sp.arcsin(-2 * (q1 * q3 - q0 * q2))
yaw = sp.arctan2(2 * (q1 * q2 + q0 * q3), (q0**2 + q1**2 - q2**2 - q3**2))
return roll, pitch, yaw
def example_theta():
pol = 'TM'
ncore = 2
nclad = 1
d = np.linspace(0.02, 3, 500) # in units of high-index wavelength
mmax = 3 # highest order of waveguide mode to consider (m = # of field antinodes)
# Beta values of each waveguide mode for each slab thickness. 0th index is slab height, 1st index is mode.
Thetas = np.zeros((len(d), mmax))
for i, di in enumerate(d):
Bs = getBetas(ncore, nclad, di, pol=pol, mmax=mmax)
Thetas[i, :] = 90 - (getTheta(Bs, ncore) * 180 / pi)
for m in range(mmax):
plt.plot(Thetas[:, m], d)
tb = sp.arctan(1 / ncore)
plt.axvline(tb * 180 / pi, color='k', ls='--')
tc = sp.arcsin(1 / ncore)
plt.axvline(tc * 180 / pi, color='y', ls='--')
plt.xlim(0, 90)
plt.xlabel('Angle (degrees)')
plt.ylabel(r'Height/$\lambda$')
plt.show()
def Finesse(d, pol='TM', m=1):
R = Ref(d, pol=pol, mode=m)
F = pi / (2 * sp.arcsin((1 - R) / (2 * R**0.5)))
F = np.nan_to_num(F)
return F
def get_bl(self, ra=None, dec=None):
"""
http://scienceworld.wolfram.com/astronomy/GalacticCoordinates.html
"""
if ra == None: ra = self.get_column("RA")
if dec == None: dec = self.get_column("DEC")
if type(ra) == float:
ral = scipy.zeros(1)
ral[0] = ra
ra = ral
if type(dec) == float:
decl = scipy.zeros(1)
decl[0] = dec
dec = decl
c62 = math.cos(62.6 * D2R)
s62 = math.sin(62.6 * D2R)
b = scipy.sin(dec * D2R) * c62
b -= scipy.cos(dec * D2R) * scipy.sin((ra - 282.25) * D2R) * s62
b = scipy.arcsin(b) * R2D
cosb = scipy.cos(b * D2R)
#l minus 33 degrees
lm33 = (scipy.cos(dec * D2R) / cosb) * scipy.cos((ra - 282.25))
l = scipy.arccos(lm33) * R2D + 33.0
return b, l
def representativeness_index_per_category(standardized_methods,
standardized_lcis):
"""
Calculates a Representativeness Index per impact category on one or many standardized LCI(s)
:param pd.DataFrame standardized_methods:
Dataframe constituted by one or many method(s) aggregated, ie. constituted by several columns representing
impact categories
:param pd.DataFrame standardized_lcis:
LCI(s) data formatted with standardize_lci()
:return:
Representativeness index per impact category
:rtype: pd.DataFrame
"""
standardized_lcis.fillna(value=0, inplace=True)
standardized_methods.fillna(value=0, inplace=True)
# Checking substance flows (indexes) are the same between lci and method
if all(standardized_methods.index == standardized_lcis.index):
representativeness_index = pd.DataFrame(
index=standardized_methods.columns,
columns=standardized_lcis.columns)
for i in range(0, representativeness_index.shape[0]):
residuals = linalg.lstsq(
sp.matrix(standardized_methods.iloc[:, i]).T,
standardized_lcis)[1]
representativeness_index.iloc[i, :] = sp.cos(
sp.real(sp.arcsin(sp.sqrt(residuals)))).T
else:
raise Exception('Substance flows do not match between method and lci.')
return representativeness_index
def rayshape_old(self, A, d, n):
# We'll get 4n+4 points, but there are duplicates at the four corners.
# So, total = 4n
rad = sp.sqrt(A/sp.pi) # the radius of the base circle
angle = sp.arcsin(1/(sp.sqrt(2) * (1+d))) # each quadrant isn't -pi/4 < theta < pi/4. A bit less than that.
base = sp.linspace(-angle, angle, n+1) # split up a quarter of the circumference to n pieces (omitting the point at pi/4)
C1 = []
for arg in base:
x = -d + (rad+d)*sp.cos(arg)
y = (rad+d)*sp.sin(arg)
C1.append((x,y))
# Construct C3, which is the image of C1 by rotation by pi.
C3 = []
for pt in C1:
C3.append((-pt[0] , -pt[1]))
# Now construct C2
base = sp.linspace(sp.pi/2 - angle, sp.pi/2 + angle, n+1) # split up a quarter of the circumference to n pieces
C2 = []
for arg in base:
x = (rad+d)*sp.cos(arg)
y = -d + (rad+d)*sp.sin(arg)
C2.append((x,y))
# Construct C4 from C2 by applying rotation by pi.
C4 = []
for pt in C2:
C4.append((-pt[0] , -pt[1]))
return sp.vstack((C1, C2, C3, C4))
def rect_to_cyl(X,Y,Z):
"""
NAME:
rect_to_cyl
PURPOSE:
convert from rectangular to cylindrical coordinates
INPUT:
X, Y, Z - rectangular coordinates
OUTPUT:
[:,3] R,phi,z
HISTORY:
2010-09-24 - Written - Bovy (NYU)
"""
R= sc.sqrt(X**2.+Y**2.)
phi= sc.arcsin(Y/R)
if isinstance(X,float) and X < 0.:
phi= m.pi-phi
elif isinstance(X,sc.ndarray):
phi[(X < 0.)]= m.pi-phi[(X < 0.)]
return (R,phi,Z)
def example_Attenuation(): ncore = 2 nclad = 1 nsub = 1 d = np.linspace(0.02,3,100) angle = np.linspace(0.02,pi/2.,100) tc = arcsin(nclad/ncore) a = np.array([Attenuation(x,ncore,nclad,nsub,y,pol='TM') for x in d for y in angle]) a = a.reshape(len(d),len(angle)) ext = [np.amin(angle)*180/pi,np.amax(angle)*180/pi,np.amin(d),np.amax(d)] plt.imshow(a.real,interpolation='nearest',origin='lower',extent=ext,aspect='auto',vmax=2000) plt.colorbar() plt.axvline(tc*180/pi,color='w',ls=':') plt.figure() plt.imshow(a.imag,interpolation='nearest',origin='lower',extent=ext,aspect='auto',vmax=2000) plt.colorbar() plt.show()
def elaz2radec_lst(el, az, lst, lat = 38.43312) :
"""DO NOT USE THIS ROUTINE FOR ANTHING THAT NEEDS TO BE RIGHT. IT DOES NOT
CORRECT FOR PRECESSION.
Calculates the Ra and Dec from elavation, aximuth, LST and Latitude.
This function is vectorized with numpy so should be fast. Standart numpy
broadcasting should also work.
All angles in degrees, lst in seconds. Latitude defaults to GBT.
"""
# Convert everything to radians.
el = sp.radians(el)
az = sp.radians(az)
lst = sp.array(lst, dtype = float)*2*sp.pi/86400
lat = sp.radians(lat)
# Calculate dec.
dec = sp.arcsin(sp.sin(el)*sp.sin(lat) +
sp.cos(el)*sp.cos(lat)*sp.cos(az))
# Calculate the hour angle
ha = sp.arccos((sp.sin(el) - sp.sin(lat)*sp.sin(dec)) /
(sp.cos(lat)*sp.cos(dec)))
ra = sp.degrees(lst - ha) % 360
return ra, sp.degrees(dec)
def get_stripe_points(mu_lim, nu_lim, r_lim, number=1): #GC checked
mu = np.random.uniform(low=mu_lim[0], high=mu_lim[1], size=number)
u, w = np.random.uniform(size=number), np.random.uniform(size=number)
nu = sc.arcsin(u * (sc.sin(nu_lim[1]) - sc.sin(nu_lim[0])) +
sc.sin(nu_lim[0]))
r = r_lim[1] * (w**(1. / 3.))
return (mu, nu, r)
def get_bl(self,ra=None,dec=None):
"""
http://scienceworld.wolfram.com/astronomy/GalacticCoordinates.html
"""
if ra==None: ra=self.get_column("RA")
if dec==None: dec=self.get_column("DEC")
if type(ra)==float:
ral=scipy.zeros(1)
ral[0]=ra
ra=ral
if type(dec)==float:
decl=scipy.zeros(1)
decl[0]=dec
dec=decl
c62=math.cos(62.6*D2R)
s62=math.sin(62.6*D2R)
b=scipy.sin(dec*D2R)*c62
b-=scipy.cos(dec*D2R)*scipy.sin((ra-282.25)*D2R)*s62
b=scipy.arcsin(b)*R2D
cosb=scipy.cos(b*D2R)
#l minus 33 degrees
lm33=(scipy.cos(dec*D2R)/cosb)*scipy.cos((ra-282.25))
l=scipy.arccos(lm33)*R2D+33.0
return b,l
def compute_and_plot(ax, n2):
xlist1 = np.linspace(-1, 0, 100)
xlist2 = np.linspace( 0, 1, 100) # cover the transmitted region
ylist_i = np.linspace(-1, 0, 100)
ylist_r = np.linspace( 0, 1, 100)
ylist = np.linspace(-1, 1, 100)
x1, y1_i = np.meshgrid(xlist1, ylist_i)
x1, y1_r = np.meshgrid(xlist1, ylist_r)
x2, y2 = np.meshgrid(xlist2, ylist)
th1 = sp.arcsin(n2/n1)
# Incident wave
Z1_i = np.cos(k1*(x1*np.cos(th1) + y1_i*np.sin(th1)))
Z1_r = np.cos(k1*(x1*np.cos(th1) - y1_r*np.sin(th1)))
# Reflected wave
Z2 = (2*n1*np.cos(th1)/(n1*np.cos(th1)+1j*sp.sqrt(n1**2*np.sin(th1)**2-1))).real*np.exp(-x2)* \
np.cos(k1*y2*np.sin(th1)) # Pulled from Griffiths Electrodynamics 4th ed.
L = np.linspace(-1.0, 0, 50)
plt.plot(L, -np.sin(th1)/np.cos(th1)*L, color='red')
plt.plot(L, np.sin(th1)/np.cos(th1)*L, color='red')
plt.vlines(0, -1, 1, colors='k')
incident = plt.contourf(x1, y1_i, Z1_i)
reflected = plt.contourf(x1, y1_r, Z1_r)
plt.colorbar(incident)
transmitted = plt.contourf(x2, y2, Z2)
def pix2sky(header,x,y): hdr_info = parse_header(header) x0 = x-hdr_info[1][0]+1. # Plus 1 python->image y0 = y-hdr_info[1][1]+1. x0 = x0.astype(scipy.float64) y0 = y0.astype(scipy.float64) x = hdr_info[2][0,0]*x0 + hdr_info[2][0,1]*y0 y = hdr_info[2][1,0]*x0 + hdr_info[2][1,1]*y0 if hdr_info[3]=="DEC": a = x.copy() x = y.copy() y = a.copy() ra0 = hdr_info[0][1] dec0 = hdr_info[0][0]/raddeg else: ra0 = hdr_info[0][0] dec0 = hdr_info[0][1]/raddeg if hdr_info[5]=="TAN": r_theta = scipy.sqrt(x*x+y*y)/raddeg theta = arctan(1./r_theta) phi = arctan2(x,-1.*y) elif hdr_info[5]=="SIN": r_theta = scipy.sqrt(x*x+y*y)/raddeg theta = arccos(r_theta) phi = artan2(x,-1.*y) ra = ra0 + raddeg*arctan2(-1.*cos(theta)*sin(phi-pi), sin(theta)*cos(dec0)-cos(theta)*sin(dec0)*cos(phi-pi)) dec = raddeg*arcsin(sin(theta)*sin(dec0)+cos(theta)*cos(dec0)*cos(phi-pi)) return ra,dec
def xyz2longlat(x,y,z):
""" converts cartesian x,y,z coordinates into spherical longitude and latitude """
r = sc.sqrt(x*x + y*y + z*z)
long = sc.arctan2(y,x)
d = sc.sqrt(x*x + y*y)
lat = sc.arcsin(z/r)
return long*deg, lat*deg, r
def pix2sky(header,x,y): hdr_info = parse_header(header) x0 = x-hdr_info[1][0]+1. # Plus 1 python->image y0 = y-hdr_info[1][1]+1. x0 = x0.astype(scipy.float64) y0 = y0.astype(scipy.float64) x = hdr_info[2][0,0]*x0 + hdr_info[2][0,1]*y0 y = hdr_info[2][1,0]*x0 + hdr_info[2][1,1]*y0 if hdr_info[3]=="DEC": a = x.copy() x = y.copy() y = a.copy() ra0 = hdr_info[0][1] dec0 = hdr_info[0][0]/raddeg else: ra0 = hdr_info[0][0] dec0 = hdr_info[0][1]/raddeg if hdr_info[5]=="TAN": r_theta = scipy.sqrt(x*x+y*y)/raddeg theta = arctan(1./r_theta) phi = arctan2(x,-1.*y) elif hdr_info[5]=="SIN": r_theta = scipy.sqrt(x*x+y*y)/raddeg theta = arccos(r_theta) phi = artan2(x,-1.*y) ra = ra0 + raddeg*arctan2(-1.*cos(theta)*sin(phi-pi), sin(theta)*cos(dec0)-cos(theta)*sin(dec0)*cos(phi-pi)) dec = raddeg*arcsin(sin(theta)*sin(dec0)+cos(theta)*cos(dec0)*cos(phi-pi)) return ra,dec
def cartesian_to_sky(position, wrap=True, degree=True):
"""Transform cartesian coordinates into distance, RA, Dec.
Parameters
----------
position : array of shape (N,3)
position in cartesian coordinates.
wrap : bool, optional
whether to wrap ra into [0,2*pi]
degree : bool, optional
whether RA, Dec are in degree (True) or radian (False).
Returns
-------
dist : array
distance.
ra : array
RA.
dec : array
Dec.
"""
dist = distance(position)
ra = scipy.arctan2(position[:, 1], position[:, 0])
if wrap: ra %= 2. * constants.pi
dec = scipy.arcsin(position[:, 2] / dist)
if degree: return dist, ra / constants.degree, dec / constants.degree
return dist, ra, dec
def __init__(self,
rarange=[0., 360.],
decrange=[-90., 90.],
nbar=None,
rng=None,
seed=None,
RA='RA',
DEC='DEC',
wrap=True,
**attrs):
area = 4 * constants.pi * (rarange[1] -
rarange[0]) / 360. / constants.degree**2
if rng is None: rng = scipy.random.RandomState(seed=seed)
self.rng = rng
size = rng.poisson(nbar * area)
ra = rng.uniform(low=rarange[0], high=rarange[1], size=size)
dec = scipy.arcsin(1. - rng.uniform(low=0, high=1, size=size) *
2.) / constants.degree
mask = (dec >= decrange[0]) & (dec <= decrange[1])
ra = ra[mask]
dec = dec[mask]
if wrap: ra %= 360.
super(RandomSkyCatalogue, self).__init__(columns={
RA: ra,
DEC: dec
},
seed=seed,
size=size,
nbar=nbar,
**attrs)
def elaz2radec_lst(el, az, lst, lat=38.43312):
"""DO NOT USE THIS ROUTINE FOR ANTHING THAT NEEDS TO BE RIGHT. IT DOES NOT
CORRECT FOR PRECESSION.
Calculates the Ra and Dec from elavation, aximuth, LST and Latitude.
This function is vectorized with numpy so should be fast. Standart numpy
broadcasting should also work.
All angles in degrees, lst in seconds. Latitude defaults to GBT.
"""
# Convert everything to radians.
el = sp.radians(el)
az = sp.radians(az)
lst = sp.array(lst, dtype=float) * 2 * sp.pi / 86400
lat = sp.radians(lat)
# Calculate dec.
dec = sp.arcsin(
sp.sin(el) * sp.sin(lat) + sp.cos(el) * sp.cos(lat) * sp.cos(az))
# Calculate the hour angle
ha = sp.arccos(
(sp.sin(el) - sp.sin(lat) * sp.sin(dec)) / (sp.cos(lat) * sp.cos(dec)))
ra = sp.degrees(lst - ha) % 360
return ra, sp.degrees(dec)
def FhklDWBA4(x,y,z,h,k,l=None,occ=None,alphai=0.2,alphaf=None,substrate=None,wavelength=1.0,e_par=0.,e_perp=1.0,gpu_name="CPU",use_fractionnal=True,language="OpenCL",cl_platform="",separate_paths=False):
"""
Calculate the grazing-incidence X-ray scattered intensity taking into account
4 scattering paths, for a nanostructure object located above a given substrate.
The 5th path is the scattering from the substrate, assumed to be below the
interface at z=0.
x,y,z: coordinates of the atoms in fractionnal coordinates (relative to the
substrate unit cell)- if use_fractionnal==False, these should be given in Angstroems
h,k,l: reciprocal space coordinates. If use_fractionnal==False, these should be given
in inverse Angstroems (multiplied by 2pi - physicist 'k' convention, |k|=4pisin(theta)/lambda,
i.e. these correspond to k_x,k_y,k_z).
alphai, alphaf: incident and outgoing angles, in radians
substrate: the substrate material, as a pynx.gid.Crystal object - this will be used
to calculate the material refraction index.
wavelength: in Angstroems
e_par,e_perp: percentage of polarisation parallel and perpendicular to the incident plane
use_fractionnal: if True (the default), then coordinates for atoms and reciprocal
space are given relatively to the unit cell, otherwise in Angstroems
and 2pi*inverse Angstroems.
Note: Either l *OR* alphaf must be supplied - it is assumed that the lattice
coordinates are such that the [001] direction is perpendicular to the surface.
"""
nrj=W2E(wavelength)
if use_fractionnal:
c=substrate.uc.parameters()[2]
s_fact=1.0
else:
c=2*pi
s_fact=1/c
if alphaf==None:
# alphaf, computed from l: l.c* = (sin(alpha_f) + sin(alpha_i))/wavelength
alphaf=scipy.arcsin(l/c*wavelength-scipy.sin(alphai))
# Incident wave
w=Wave(alphai,e_par,e_perp,nrj)
dw=DistortedWave(None,substrate,w)
# Reflected wave after the dot
w1=Wave(alphaf,e_par,e_perp,nrj)
dw1=DistortedWave(None,substrate,w1)
# First path, direct diffraction
l=c*scipy.sin(alphaf+alphai)/wavelength
f1=gpu.Fhkl_thread(h*s_fact,k*s_fact,l*s_fact,x,y,z,occ=occ,gpu_name=gpu_name,language=language,cl_platform=cl_platform)[0]
# Second path, reflection before
l=c*scipy.sin(alphaf-alphai)/wavelength
f2=gpu.Fhkl_thread(h*s_fact,k*s_fact,l*s_fact,x,y,z,occ=occ,gpu_name=gpu_name,language=language,cl_platform=cl_platform)[0]*dw.Riy
# Third path, reflection after dot
l=c*scipy.sin(-alphaf+alphai)/wavelength
f3=gpu.Fhkl_thread(h*s_fact,k*s_fact,l*s_fact,x,y,z,occ=occ,gpu_name=gpu_name,language=language,cl_platform=cl_platform)[0]*dw1.Riy
# Fourth path, reflection before and after dot
l=c*scipy.sin(-alphaf-alphai)/wavelength
f4=gpu.Fhkl_thread(h*s_fact,k*s_fact,l*s_fact,x,y,z,occ=occ,gpu_name=gpu_name,language=language,cl_platform=cl_platform)[0]*dw.Riy*dw1.Riy
if separate_paths: return f1,f2,f3,f4
return f1+f2+f3+f4
def sin_seq(A = 1.0, f = 1.0, T = 1.0, delta = 0.1):
t = 0.0
events = []
# Note use of round() to compensate for floating-point arithmetic errors
# that lead to inexact results.
while t <= T:
v = delta * floor(round(A*sin(2*pi*f*t) / delta,10))
events += [(t, v)]
tm = fmod(abs(t), 0.5/f)
if tm < 0.25/f:
vq = delta * (floor(round(A*sin(2*pi*f*tm) / delta,10)) + 1.0)
dt = arcsin(vq/A)/(2*pi*f) - tm
else:
vq = delta * (floor(round(A*sin(2*pi*f*tm) / delta,10)) - 1.0)
dt = (pi - arcsin(vq/A))/(2*pi*f) - tm
t += dt
return array(events)
def _arcsin_sqrt_transform(values):
a = sp.array(values)
if min(a) < 0 or max(a) > 1:
logger.debug('Some values are outside of range [0,1], hence skipping transformation!')
return None
else:
vals = sp.arcsin(sp.sqrt(a))
return vals
def azimuth(self, date):
dec = self.declination(date)
ha = self.hour_angle(date)
az = sp.arcsin(sp.cos(dec) * sp.sin(ha) / sp.cos(self.elevation(date)))
if (sp.cos(ha) >= (sp.tan(dec) / sp.tan(self.lat))):
return az
else:
return (sp.pi - az)
def theta_def(theta_i, p, m):
'''输入的theta 是度数不是弧度,得到的是偏转角'''
theta_i = theta_i * pi / 180
theta_r = arcsin(sin(theta_i) / m)
ths = (2 * p * theta_r - 2 * theta_i - (p - 1) * pi)
ths = real(ths)
res = ths * 180 / pi
return res
def test_healpix_sphere(self):
# Sphere parameters.
R = 5
# Expected outputs of healpix_sphere() applied to inputs.
sigma_a = sqrt(3 - 3*sin(a[1]))
ha = (pi/4*(1 - sigma_a), pi/4*(2 - sigma_a))
hb = (ha[0], -ha[1])
healpix_sphere_outputs = [
(0, 0),
(0, pi/4),
(0, -pi/4),
(pi/2, 0),
(-pi/2, 0),
(-pi, 0),
(-3*pi/4, pi/2),
(-3*pi/4, -pi/2),
ha,
hb
]
healpix_sphere_outputs = [tuple(R*array(p)) for p in
healpix_sphere_outputs]
# Forward projection should be correct on test points.
f = Proj(proj='healpix', R=R)
given = inputs
get = [f(*p, radians=True) for p in given]
expect = healpix_sphere_outputs
# Fuzz to allow for rounding errors:
error = 1e-12
print
print '='*80
print 'HEALPix forward projection, sphere with radius R = %s' % R
print 'input (radians) / expected output (meters) / received output'
print '='*80
for i in range(len(get)):
print given[i], expect[i], get[i]
self.assertTrue(rel_err(get[i], expect[i]) < error)
# Inverse of projection of a point p should yield p.
given = get
get = [f(*q, radians=True, inverse=True) for q in given]
expect = inputs
print '='*80
print 'HEALPix inverse projection, sphere with radius R = %s' % R
print 'input (meters) / expected output (radians) / received output'
print '='*80
for i in range(len(get)):
print given[i], expect[i], get[i]
self.assertTrue(rel_err(get[i], expect[i]) < error)
# Inverse projection of p below should return longitude of -pi.
# Previously, it was returning a number slightly less than pi
# because of a rounding error, which got magnified by
# wrap_longitude()
p = R*array((-7*pi/8, 3*pi/8))
get = f(*p, radians=True, inverse=True)
expect = (-pi, arcsin(1 - 1.0/12))
self.assertTrue(rel_err(get, expect) < error)
def _arcsin_sqrt_transform(self, verbose=False):
a = sp.array(self.values)
if min(a) < 0 or max(a) > 1:
log.debug('Some values are outside of range [0,1], hence skipping transformation!')
return False
else:
vals = sp.arcsin(sp.sqrt(a))
self._perform_transform(vals,"arcsin")
return True
def law_xyz2sgr_gal(X, Y, Z, Xsun=dsun):
""" From the Law sgr transformation code: http://www.astro.virginia.edu/~srm4n/Sgr/code.html
// Transform positions from standard left handed Galactocentric XYZ to [RIGHT-HANDED]
// the Galactocentric Sgr system (lambda=0 at the Galactic plane)
// Input must be in kpc of the form X Y Z
// Output is in kpc and degrees, of the form X_Sgr,GC Y_Sgr,GC Z_Sgr,GC d_GC lambda_GC beta_GC
// Note that d is distance from Galactic Center"""
radpdeg = 3.141592653589793 / 180.0
#// Define the Euler angles
phi = (180 + 3.75) * radpdeg
theta = (90 - 13.46) * radpdeg
psiGC = (180 + 21.604399) * radpdeg
#// Rotation angle of phiGC past 180degrees is a useful number
ang = 21.604399 * radpdeg
#// Note that the plane does not actually include the G.C., although it is close
xcenter = -8.5227
ycenter = -0.3460
zcenter = -0.0828
#// Define the rotation matrix from the Euler angles
GCrot11 = sc.cos(psiGC) * sc.cos(phi) - sc.cos(theta) * sc.sin(
phi) * sc.sin(psiGC)
GCrot12 = sc.cos(psiGC) * sc.sin(phi) + sc.cos(theta) * sc.cos(
phi) * sc.sin(psiGC)
GCrot13 = sc.sin(psiGC) * sc.sin(theta)
GCrot21 = -sc.sin(psiGC) * sc.cos(phi) - sc.cos(theta) * sc.sin(
phi) * sc.cos(psiGC)
GCrot22 = -sc.sin(psiGC) * sc.sin(phi) + sc.cos(theta) * sc.cos(
phi) * sc.cos(psiGC)
GCrot23 = sc.cos(psiGC) * sc.sin(theta)
GCrot31 = sc.sin(theta) * sc.sin(phi)
GCrot32 = -sc.sin(theta) * sc.cos(phi)
GCrot33 = sc.cos(theta)
#X = -X #// Make the input system right-handed ALREADY IS
X = X + Xsun #// Transform the input system to heliocentric right handed coordinates
#// Calculate Z,distance in the SgrGC system
Temp = GCrot11 * (X + xcenter) + GCrot12 * (Y - ycenter) + GCrot13 * (
Z - zcenter)
Temp2 = GCrot21 * (X + xcenter) + GCrot22 * (Y - ycenter) + GCrot23 * (
Z - zcenter)
Zs = GCrot31 * (X + xcenter) + GCrot32 * (Y - ycenter) + GCrot33 * (
Z - zcenter)
d = sc.sqrt(Temp * Temp + Temp2 * Temp2 + Zs * Zs)
Zs = -Zs
#// Calculate the angular coordinates lambdaGC,betaGC
Temp3 = sc.arctan2(Temp2, Temp) / radpdeg
if (Temp3 < 0.0): Temp3 = Temp3 + 360.0
Temp3 = Temp3 + ang / radpdeg
if (Temp3 > 360.0): Temp3 = Temp3 - 360.0
lam = Temp3
beta = sc.arcsin(
Zs / sc.sqrt(Temp * Temp + Temp2 * Temp2 + Zs * Zs)) / radpdeg
#// Calculate X,Y in the SgrGC system
Xs = Temp * sc.cos(ang) - Temp2 * sc.sin(ang)
Ys = Temp * sc.sin(ang) + Temp2 * sc.cos(ang)
r = sc.sqrt(Xs * Xs + Ys * Ys + Zs + Zs)
return Xs, Ys, Zs, lam, beta, r
def sky2pix(header,ra,dec): hdr_info = parse_header(header) if scipy.isscalar(ra): ra /= raddeg dec /= raddeg else: ra = ra.astype(scipy.float64)/raddeg dec = dec.astype(scipy.float64)/raddeg if hdr_info[3]=="DEC": ra0 = hdr_info[0][1]/raddeg dec0 = hdr_info[0][0]/raddeg else: ra0 = hdr_info[0][0]/raddeg dec0 = hdr_info[0][1]/raddeg phi = pi + arctan2(-1*cos(dec)*sin(ra-ra0),sin(dec)*cos(dec0)-cos(dec)*sin(dec0)*cos(ra-ra0)) argtheta = sin(dec)*sin(dec0)+cos(dec)*cos(dec0)*cos(ra-ra0) if scipy.isscalar(argtheta): theta = arcsin(argtheta) else: argtheta[argtheta>1.] = 1. theta = arcsin(argtheta) if hdr_info[5]=="TAN": r_theta = raddeg/tan(theta) x = r_theta*sin(phi) y = -1.*r_theta*cos(phi) elif hdr_info[5]=="SIN": r_theta = raddeg*cos(theta) x = r_theta*sin(phi) y = -1.*r_theta*cos(phi) if hdr_info[3]=="DEC": a = x.copy() x = y.copy() y = a.copy() inv = linalg.inv(hdr_info[2]) x0 = inv[0,0]*x + inv[0,1]*y y0 = inv[1,0]*x + inv[1,1]*y x = x0+hdr_info[1][0]-1 y = y0+hdr_info[1][1]-1 return x,y
def sky2pix(header,ra,dec): hdr_info = parse_header(header) if scipy.isscalar(ra): ra /= raddeg dec /= raddeg else: ra = ra.astype(scipy.float64)/raddeg dec = dec.astype(scipy.float64)/raddeg if hdr_info[3]=="DEC": ra0 = hdr_info[0][1]/raddeg dec0 = hdr_info[0][0]/raddeg else: ra0 = hdr_info[0][0]/raddeg dec0 = hdr_info[0][1]/raddeg phi = pi + arctan2(-1*cos(dec)*sin(ra-ra0),sin(dec)*cos(dec0)-cos(dec)*sin(dec0)*cos(ra-ra0)) argtheta = sin(dec)*sin(dec0)+cos(dec)*cos(dec0)*cos(ra-ra0) if scipy.isscalar(argtheta): theta = arcsin(argtheta) else: argtheta[argtheta>1.] = 1. theta = arcsin(argtheta) if hdr_info[5]=="TAN": r_theta = raddeg/tan(theta) x = r_theta*sin(phi) y = -1.*r_theta*cos(phi) elif hdr_info[5]=="SIN": r_theta = raddeg*cos(theta) x = r_theta*sin(phi) y = -1.*r_theta*cos(phi) if hdr_info[3]=="DEC": a = x.copy() x = y.copy() y = a.copy() inv = linalg.inv(hdr_info[2]) x0 = inv[0,0]*x + inv[0,1]*y y0 = inv[1,0]*x + inv[1,1]*y x = x0+hdr_info[1][0]-1 y = y0+hdr_info[1][1]-1 return x,y
def OnSomethingChanged(self):
nOne = self.sldRIOne.value() / 100
nTwo = self.sldRITwo.value() / 100
incAng = self.sldIncAng.value()
refrAng = 180.0 / pi * arcsin(nOne * sin(pi / 180.0 * incAng) / nTwo)
if isinstance(refrAng, complex):
self.edtRefrAng.setText('Total Internal Reflection')
else:
self.edtRefrAng.setText(str('%5.3f' % (refrAng)))
self.loCanvas.drawPlot(nOne, nTwo, incAng)
def cart2sphere(coordlist):
X_vec = coordlist[:,0]
Y_vec = coordlist[:,1]
Z_vec = coordlist[:,2]
R_vec = sp.sqrt(X_vec**2+Y_vec**2+Z_vec**2)
Az_vec = np.degrees(sp.arctan2(X_vec,Y_vec))
El_vec = np.degrees(sp.arcsin(Z_vec/R_vec))
sp_coords = sp.array([R_vec,Az_vec,El_vec]).transpose()
return sp_coords
def list_snell(n_list, th_0):
"""
return list of angle theta in each layer based on angle th_0 in layer 0,
using Snell's law. n_list is index of refraction of each layer. Note that
"angles" may be complex!!
"""
#Important that the arcsin here is scipy.arcsin, not numpy.arcsin!! (They
#give different results e.g. for arcsin(2).)
#Use real_if_close because e.g. arcsin(2 + 1e-17j) is very different from
#arcsin(2) due to branch cut
return sp.arcsin(np.real_if_close(n_list[0] * np.sin(th_0) / n_list))
def snell(n_1, n_2, th_1):
"""
return angle theta in layer 2 with refractive index n_2, assuming
it has angle th_1 in layer with refractive index n_1. Use Snell's law. Note
that "angles" may be complex!!
"""
#Important that the arcsin here is scipy.arcsin, not numpy.arcsin!! (They
#give different results e.g. for arcsin(2).)
#Use real_if_close because e.g. arcsin(2 + 1e-17j) is very different from
#arcsin(2) due to branch cut
return sp.arcsin(np.real_if_close(n_1 * np.sin(th_1) / n_2))
def list_snell(n_list,th_0):
"""
return list of angle theta in each layer based on angle th_0 in layer 0,
using Snell's law. n_list is index of refraction of each layer. Note that
"angles" may be complex!!
"""
#Important that the arcsin here is scipy.arcsin, not numpy.arcsin!! (They
#give different results e.g. for arcsin(2).)
#Use real_if_close because e.g. arcsin(2 + 1e-17j) is very different from
#arcsin(2) due to branch cut
return sp.arcsin(np.real_if_close((n_list[:,0]*np.sin(th_0))[:,None] / n_list))
def snell(n_1, n_2, th_1):
"""
Return angle theta in layer 2 with refractive index n_2, assuming
it has angle th_1 in layer with refractive index n_1. Use Snell's law. Note
that "angles" may be complex!!
"""
# Important that the arcsin here is scipy.arcsin, not numpy.arcsin!! (They
# give different results e.g. for arcsin(2).)
# Use real_if_close because e.g. arcsin(2 + 1e-17j) is very different from
# arcsin(2) due to branch cut
return sp.arcsin(np.real_if_close(n_1 * np.sin(th_1) / n_2))
def cart2sphere(coordlist):
r2d = 180.0/sp.pi
d2r = sp.pi/180.0
X_vec = coordlist[:,0]
Y_vec = coordlist[:,1]
Z_vec = coordlist[:,2]
R_vec = sp.sqrt(X_vec**2+Y_vec**2+Z_vec**2)
Az_vec = sp.arctan2(X_vec,Y_vec)*r2d
El_vec = sp.arcsin(Z_vec/R_vec)*r2d
sp_coords = sp.array([R_vec,Az_vec,El_vec]).transpose()
return sp_coords
def snell(n_1,n_2,th_1):
"""
return angle theta in layer 2 with refractive index n_2, assuming
it has angle th_1 in layer with refractive index n_1. Use Snell's law. Note
that "angles" may be complex!!
"""
#Important that the arcsin here is scipy.arcsin, not numpy.arcsin! (They
#give different results e.g. for arcsin(2).)
th_2_guess = sp.arcsin(n_1*np.sin(th_1) / n_2)
if is_forward_angle(n_2, th_2_guess):
return th_2_guess
else:
return pi - th_2_guess
def lbToEq (l_deg, b_deg):
""" Converts galactic l,b in to Equatorial ra, dec; from Binney and Merrifield, p. 31;
l, b must be arrays of same shape"""
l, b = (l_deg*rad), (b_deg*rad)
# Conversion Code
t = lCP - l
dec = sc.arcsin(sc.sin(decGP)*sc.sin(b) + sc.cos(decGP)*sc.cos(b)*sc.cos(t) )
r = sc.arctan2( (sc.cos(b)*sc.sin(t)),
( (sc.cos(decGP)*sc.sin(b)) - (sc.sin(decGP)*sc.cos(b)*sc.cos(t))) )
if type(r) != type(arr): r = sc.array([r])
for i in range(len(r)):
r[i] = angle_bounds((r[i] + raGP)*deg)
return r, (dec*deg)
def EqTolb (ra_deg, dec_deg):
""" Converts equatorial ra, dec, into galactic l,b; from Binney and Merrifield, p. 31
following the method of http://star-www.st-and.ac.uk/~spd3/Teaching/AS3013/programs/radec2lb.f90
NOT QUITE - I use arctan2 method instead"""
ra, dec = (ra_deg*rad), (dec_deg*rad)
# Conversion Code
r = (ra - raGP)
b = sc.arcsin( sc.sin(decGP)*sc.sin(dec) + sc.cos(decGP)*sc.cos(dec)*sc.cos(r) )
t = sc.arctan2((sc.cos(dec)*sc.sin(r)),
(sc.cos(decGP)*sc.sin(dec) - sc.sin(decGP)*sc.cos(dec)*sc.cos(r)) )
l = (lCP - t)
b, l = angle_bounds2((b*deg), (l*deg))
return l, b
def T_ps_rl(m_t_ps,theta_0,n_0,n_s):
'''Utility to compute transmittance for p,s and right.left
circular polarization
Parameters
----------
'm_t_ps' = ps transmission matrix
Returns
-------
'a dictionary' = {'T_p':T_p, #transmittances
'T_s':T_s,
'T_l':T_l,
'T_r':T_r
'A_p':-np.log10(T_p), #absorbances
'A_s':-np.log10(T_s),
'A_r':-np.log10(T_r),
'A_l':-np.log10(T_l)}
'''
# extracting values from the matrix
t_pp = m_t_ps[0,0]
t_ps = m_t_ps[0,1]
t_sp = m_t_ps[1,0]
t_ss = m_t_ps[1,1]
# calculating the transmittance
theta_s = sp.arcsin(np.real_if_close(np.sin(theta_0)*n_0/n_s))
norm = (np.real(n_s*np.conj(np.cos(theta_s))) /
np.real(n_0*np.conj(np.cos(theta_0))))
T_p = norm*(np.abs(t_pp)**2 + np.abs(t_sp)**2)
T_s = norm*(np.abs(t_ss)**2 + np.abs(t_ps)**2)
T_r = 0.5*norm*(np.abs(t_pp)**2 + np.abs(t_ss)**2 +
np.abs(t_sp)**2 + np.abs(t_ps)**2 +
2.0*np.real(1j*t_pp*np.conj(t_ps)) +
2.0*np.real(1j*t_sp*np.conj(t_ss)))
T_l = 0.5*norm*(np.abs(t_pp)**2 + np.abs(t_ss)**2 +
np.abs(t_sp)**2 + np.abs(t_ps)**2 -
2.0*np.real(1j*t_pp*np.conj(t_ps)) -
2.0*np.real(1j*t_sp*np.conj(t_ss)))
out_dict = {'T_p':T_p,
'T_s':T_s,
'T_l':T_l,
'T_r':T_r,
'A_p':-np.log10(T_p),
'A_s':-np.log10(T_s),
'A_r':-np.log10(T_r),
'A_l':-np.log10(T_l)}
return out_dict
def purcell(physics,
network,
geometry,
fluid,
propname,
r_toroid,
pore_surface_tension='surface_tension',
pore_contact_angle='contact_angle',
throat_diameter='diameter',
**params):
r"""
Computes the throat capillary entry pressure assuming the throat is a toroid.
Parameters
----------
network : OpenPNM Network Object
The network on which to apply the calculation
sigma : float, array_like
Surface tension of the invading/defending fluid pair. Units must be consistent with the throat size values, but SI is encouraged.
theta : float, array_like
Contact angle formed by a droplet of the invading fluid and solid surface, measured through the defending fluid phase. Angle must be given in degrees.
r_toroid : float or array_like
The radius of the solid
Notes
-----
This approach accounts for the converging-diverging nature of many throat types. Advancing the meniscus beyond the apex of the toroid requires an increase in capillary pressure beyond that for a cylindical tube of the same radius. The details of this equation are described by Mason and Morrow [1]_, and explored by Gostick [2]_ in the context of a pore network model.
References
----------
.. [1] G. Mason, N. R. Morrow, Effect of contact angle on capillary displacement curvatures in pore throats formed by spheres. J. Colloid Interface Sci. 168, 130 (1994).
.. [2] J. Gostick, Random pore network modeling of fibrous PEMFC gas diffusion media using Voronoi and Delaunay tessellations. J. Electrochem. Soc. 160, F731 (2013).
"""
#This seesm to work, but I wrote it quickly and lost track of the degree-radians conversions
"""TODO:
Triple check the accuracy of this equation
"""
sigma = network.get_pore_data(phase=fluid,prop=pore_surface_tension)
sigma = network.interpolate_throat_data(sigma)
theta = network.get_pore_data(phase=fluid,prop=pore_contact_angle)
theta = network.interpolate_throat_data(theta)
r = network.get_throat_data(prop=throat_diameter)/2
R = r_toroid
alpha = theta - 180 + sp.arcsin(sp.sin(sp.radians(theta)/(1+r/R)))
value = (-2*sigma/r)*(sp.cos(sp.radians(theta - alpha))/(1 + R/r*(1-sp.cos(sp.radians(alpha)))))
mask = network.get_throat_indices(geometry)
network.set_throat_data(phase=fluid,prop=propname,data=value[mask],locations=geometry)
def arcsin_sqrt_transform(self, pid, verbose=False):
a = sp.array(self.phen_dict[pid]["values"])
if min(a) < 0 or max(a) > 1:
if verbose:
print "Some values are outside of range [0,1], hence skipping transformation!"
return False
else:
vals = sp.arcsin(sp.sqrt(a))
if not self.phen_dict[pid]["transformation"]:
self.phen_dict[pid]["raw_values"] = self.phen_dict[pid]["values"]
self.phen_dict[pid]["transformation"] = "arcsin_sqrt"
else:
self.phen_dict[pid]["transformation"] = "arcsin_sqrt(" + self.phen_dict[pid]["transformation"] + ")"
self.phen_dict[pid]["values"] = vals.tolist()
return True
def arcsin_sqrt_transform(self, pid, verbose=False):
a = sp.array(self.phen_dict[pid]['values'])
if min(a) < 0 or max(a) > 1:
if verbose:
print 'Some values are outside of range [0,1], hence skipping transformation!'
return False
else:
vals = sp.arcsin(sp.sqrt(a))
if not self.phen_dict[pid]['transformation']:
self.phen_dict[pid]['raw_values'] = self.phen_dict[pid]['values']
self.phen_dict[pid]['transformation'] = 'arcsin_sqrt'
else:
self.phen_dict[pid]['transformation'] = 'arcsin_sqrt(' + self.phen_dict[pid]['transformation'] + ')'
self.phen_dict[pid]['values'] = vals.tolist()
return True
def rotmat_from_u2v(u,v):
"""
Return the rotation matrix associated with rotation of vector u onto vector v. Euler-Rodrigues formula.
"""
u, v = u / LA.norm(u), v / LA.norm(v)
axis = sp.cross(u,v)
theta = sp.arcsin(LA.norm(axis))
axis = axis/LA.norm(axis) # math.sqrt(np.dot(axis, axis))
a = sp.cos(theta/2)
b, c, d = -axis * sp.sin(theta/2)
aa, bb, cc, dd = 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([[aa+bb-cc-dd, 2*(bc+ad), 2*(bd-ac)],
[2*(bc-ad), aa+cc-bb-dd, 2*(cd+ab)],
[2*(bd+ac), 2*(cd-ab), aa+dd-bb-cc]])
def law_xyz2sgr_gal(X,Y,Z, Xsun=dsun):
""" From the Law sgr transformation code: http://www.astro.virginia.edu/~srm4n/Sgr/code.html
// Transform positions from standard left handed Galactocentric XYZ to [RIGHT-HANDED]
// the Galactocentric Sgr system (lambda=0 at the Galactic plane)
// Input must be in kpc of the form X Y Z
// Output is in kpc and degrees, of the form X_Sgr,GC Y_Sgr,GC Z_Sgr,GC d_GC lambda_GC beta_GC
// Note that d is distance from Galactic Center"""
radpdeg = 3.141592653589793/180.0
#// Define the Euler angles
phi = (180+3.75)*radpdeg
theta = (90-13.46)*radpdeg
psiGC = (180+21.604399)*radpdeg
#// Rotation angle of phiGC past 180degrees is a useful number
ang = 21.604399*radpdeg
#// Note that the plane does not actually include the G.C., although it is close
xcenter = -8.5227
ycenter = -0.3460
zcenter = -0.0828
#// Define the rotation matrix from the Euler angles
GCrot11 = sc.cos(psiGC)*sc.cos(phi)-sc.cos(theta)*sc.sin(phi)*sc.sin(psiGC)
GCrot12 = sc.cos(psiGC)*sc.sin(phi)+sc.cos(theta)*sc.cos(phi)*sc.sin(psiGC)
GCrot13 = sc.sin(psiGC)*sc.sin(theta)
GCrot21 = -sc.sin(psiGC)*sc.cos(phi)-sc.cos(theta)*sc.sin(phi)*sc.cos(psiGC)
GCrot22 = -sc.sin(psiGC)*sc.sin(phi)+sc.cos(theta)*sc.cos(phi)*sc.cos(psiGC)
GCrot23 = sc.cos(psiGC)*sc.sin(theta)
GCrot31 = sc.sin(theta)*sc.sin(phi)
GCrot32 = -sc.sin(theta)*sc.cos(phi)
GCrot33 = sc.cos(theta)
#X = -X #// Make the input system right-handed ALREADY IS
X = X + Xsun #// Transform the input system to heliocentric right handed coordinates
#// Calculate Z,distance in the SgrGC system
Temp=GCrot11*(X+xcenter)+GCrot12*(Y-ycenter)+GCrot13*(Z-zcenter)
Temp2=GCrot21*(X+xcenter)+GCrot22*(Y-ycenter)+GCrot23*(Z-zcenter)
Zs=GCrot31*(X+xcenter)+GCrot32*(Y-ycenter)+GCrot33*(Z-zcenter)
d=sc.sqrt(Temp*Temp+Temp2*Temp2+Zs*Zs)
Zs=-Zs;
#// Calculate the angular coordinates lambdaGC,betaGC
Temp3 = sc.arctan2(Temp2,Temp)/radpdeg;
if (Temp3 < 0.0): Temp3 = Temp3 + 360.0
Temp3 = Temp3 + ang/radpdeg
if (Temp3 > 360.0): Temp3 = Temp3 - 360.0
lam = Temp3
beta = sc.arcsin(Zs/sc.sqrt(Temp*Temp+Temp2*Temp2+Zs*Zs))/radpdeg
#// Calculate X,Y in the SgrGC system
Xs=Temp*sc.cos(ang) - Temp2*sc.sin(ang)
Ys=Temp*sc.sin(ang) + Temp2*sc.cos(ang)
r = sc.sqrt(Xs*Xs + Ys*Ys + Zs+Zs)
return Xs, Ys, Zs, lam, beta, r
def list_snell(n_list,th_0):
"""
return list of angle theta in each layer based on angle th_0 in layer 0,
using Snell's law. n_list is index of refraction of each layer. Note that
"angles" may be complex!!
"""
#Important that the arcsin here is scipy.arcsin, not numpy.arcsin! (They
#give different results e.g. for arcsin(2).)
angles = sp.arcsin(n_list[0]*np.sin(th_0) / n_list)
# the first and last entry need to be the forward angle (the intermediate
# layers don't matter, see https://arxiv.org/abs/1603.02720 Section 5)
if not is_forward_angle(n_list[0], angles[0]):
angles[0] = pi - angles[0]
if not is_forward_angle(n_list[-1], angles[-1]):
angles[-1] = pi - angles[-1]
return angles
def GCToEq (mu_deg, nu_deg, wedge): # produces lists.... ROTATE
""" Converts Stripe mu, nu into equatorial ra, dec. Called 'atGCToEq' in at SurveyGeometry.c"""
node = (surveyCenterRa - 90.0)*rad
eta = get_eta(wedge)
inc = (surveyCenterDec + eta)*rad
mu, nu = (mu_deg*rad), (nu_deg*rad)
# Rotation
x2 = sc.cos(mu - node)*sc.cos(nu)
y2 = sc.sin(mu - node)*sc.cos(nu)
z2 = sc.sin(nu)
x1 = x2
y1 = y2*sc.cos(inc) - z2*sc.sin(inc)
z1 = y2*sc.sin(inc) + z2*sc.cos(inc)
ra = sc.arctan2(y1,x1) + node
dec = sc.arcsin(z1)
dec, ra = angle_bounds2((dec*deg),(ra*deg))
return ra, dec