def reset(self):
self.post = gv_general.chiwedge( wedge = self.pars.get('wedge'),
chi = self.pars.get('chi')).ravel()
self.posti= np.dot(gv_general.wedgemat(self.pars.get('wedge')),
gv_general.chimat(self.pars.get('chi'))).T.ravel()
self.axis = np.array([0,0,-1],np.float)
def grain_x0(omega, wedge, chi, tx, ty, tz):
""" Grain origin positions at Omega rotation """
co = np.cos(np.radians(omega))
so = np.sin(np.radians(omega))
x0 = np.zeros((3, omega.shape[0]))
x0[0] = co * tx - so * ty
x0[1] = so * tx + co * ty
x0[2] = tz
cw = gv_general.chiwedge(chi, wedge)
x0 = np.dot(cw.T, x0)
return x0
def g_to_k(g, omega, wedge, chi):
""" Rotate g vector to k vector """
co = np.cos(np.radians(omega))
so = np.sin(np.radians(omega))
k = np.zeros((3, len(omega)))
k[0, :] = co * g[0, :] - so * g[1, :]
k[1, :] = so * g[0, :] + co * g[1, :]
k[2, :] = g[2, :]
cw = gv_general.chiwedge(chi, wedge)
k = np.dot(cw, k)
return k
def k_to_g(k, omega, wedge, chi):
""" Rotate k vector to g vector """
#print "k_to_g",k,omega,wedge,chi
om = np.radians(omega)
g = np.zeros(k.shape)
cw = gv_general.chiwedge(chi, wedge)
cwk = np.dot(cw, k)
co = np.cos(np.radians(omega)) # 1D
so = np.sin(np.radians(omega)) # 1D
g[0, :] = co * cwk[0, :] + so * cwk[1, :]
g[1, :] = -so * cwk[0, :] + co * cwk[1, :]
g[2, :] = cwk[2, :]
return g
def compute_XLYLZL(self):
self.peaks_xyz = transform.compute_xyz_lab(
[self.colfile.sc, self.colfile.fc],
**self.colfile.parameters.parameters)
# These are the peak positions in the laboratory frame
#
# Now get the beam and peaks in the crystal frame
wedge = float(self.colfile.parameters.get('wedge'))
chi = float(self.colfile.parameters.get('chi'))
self.chiwedge = gv_general.chiwedge(chi, wedge)
omega = np.radians(self.colfile.omega)
cosomega = np.cos(omega)
sinomega = np.sin(omega)
beam = np.zeros((3, len(omega)), float)
beam[0, :] = 1.
self.XB = k_to_g(beam, cosomega, sinomega, self.chiwedge)
self.XS = k_to_g(self.peaks_xyz, cosomega, sinomega, self.chiwedge)
def testhklcalc_many(wedge, chi):
# hklcalc_many
# apply wedge, chi to axis if necessary
axis = np.array( [0,0,-1], np.float )
UBI = np.eye(3).ravel()
hkl = np.zeros( (len(omega), 3), np.float)
XL = np.ones( (len(omega), 3), np.float)*1e3
T = np.array([100,200,300],np.float)
wvln = 0.254
pre = np.eye(3).ravel()
post = gv_general.chiwedge( wedge=wedge, chi=chi ).ravel()
kc = XL.copy()
wripaca.hklcalc_many( XL, axis, omega*np.pi/180, UBI, T, pre, post, hkl, wvln, kc)
print "axis is",axis
t, e = transform.compute_tth_eta_from_xyz( XL.T,
t_x = T[0],
t_y = T[1],
t_z = T[2],
omega = omega,
wedge = wedge,
chi = chi
)
#print t,e,omega
ori = transform.compute_grain_origins( omega, wedge=wedge, chi=chi,
t_x = T[0], t_y = T[1], t_z = T[2] )
print "last origin",ori.T[-1],ori.T[0]
print "last xl",XL[-1],XL[0]
kve = transform.compute_k_vectors( t, e, wvln )
print "last k",kve.T[-1],kve.T[0]
gve = transform.compute_g_vectors( t, e, omega, wvln, wedge=wedge, chi=chi )
print "last g",gve.T[-1],gve.T[0]
htest = np.dot( UBI.reshape(3,3), gve )
for i in range(len(t)):
# print gve[:,i]
# print hkl[i]
if ((gve[:,i]-hkl[i])**2).sum() > 1e-10:
print "FAIL",
print i,gve[:,i],hkl[i],((gve[:,i]-hkl[i])**2).sum()
print wedge,chi
sys.exit()
print "OK for wedge",wedge,"chi",chi
def test_25_30(self):
""" wedge, chi = 25,30 """
w, c = 25, 30
SANITY = False
if SANITY: print "*" * 80
om = np.zeros(self.np, np.float)
g_old = transform.compute_g_vectors(self.tth,
self.eta,
self.omega,
self.wvln,
wedge=w,
chi=c)
if SANITY: print g_old.shape, "\n", g_old[:, :3]
k = transform.compute_k_vectors(self.tth, self.eta, self.wvln)
if SANITY: print "k=", k[:, :3]
post = gv_general.chiwedge(chi=c, wedge=w)
g_new = gv_general.k_to_g(k, self.omega, axis=[0, 0, -1], post=post)
if SANITY: print g_new.shape, g_new[:, :3]
if SANITY: print "end routine"
if SANITY: print "*" * 80
self.assertAlmostEqual(array_diff(g_new, g_old), 0, 6)
def uncompute_g_vectors(g, wavelength, wedge=0.0, chi=0.0):
"""
Given g-vectors compute tth,eta,omega
assert uncompute_g_vectors(compute_g_vector(tth,eta,omega))==tth,eta,omega
"""
if wedge == chi == 0:
post = None
else:
post = gv_general.wedgechi(wedge=wedge, chi=chi)
omega1, omega2, valid = gv_general.g_to_k(g,
wavelength,
axis=[0, 0, -1],
pre=None,
post=post)
# we know g, omega. Compute k as ... ?
if post is None:
pre = None
else:
pre = gv_general.chiwedge(wedge=wedge, chi=chi).T
k_one = gv_general.k_to_g(g, omega1, axis=[0, 0, 1], pre=pre, post=None)
k_two = gv_general.k_to_g(g, omega2, axis=[0, 0, 1], pre=pre, post=None)
#
# k[1,:] = -ds*c*sin(eta)
# ------ ------------- .... tan(eta) = -k1/k2
# k[2,:] = ds*c*cos(eta)
#
eta_one = np.arctan2(-k_one[1, :], k_one[2, :])
eta_two = np.arctan2(-k_two[1, :], k_two[2, :])
#
#
ds = np.sqrt(np.sum(g * g, 0))
s = ds * wavelength / 2.0 # sin theta
tth = np.degrees(np.arcsin(s) * 2.) * valid
eta1 = np.degrees(eta_one) * valid
eta2 = np.degrees(eta_two) * valid
omega1 = omega1 * valid
omega2 = omega2 * valid
return tth, [eta1, eta2], [omega1, omega2]
def Dcalc(UB, hkls, wedge, chi, wavelength, etao, omega):
"""
Finds "C"alculated 2thetac, etac, omegac for a grain
(Note that these do not depend on the grain position)
UB = 3x3 UB matrix
hkls = 3xn list of peaks (normally integers)
wedge = tilt around y under rotation axis
chi = tilt around beam under rotation axis
wavelength = of the radiation, scales UB
etao = observed azimuth values (angle on powder ring)
omega = observed(?) sample rotation angles
??? ysign determines which solution (there are usually two)
"""
# computed g-vectors
g = np.dot(UB, hkls)
assert g.dtype == float
if 0:
print(g.shape)
print(hkls.shape)
for i in range(10):
print(g[:, i], end=' ')
print(hkls[:, i], end=' ')
print(np.dot(np.linalg.inv(UB), g[:, i]))
# wedge/chi matrix for axis orientation
wc = gv_general.wedgechi(wedge=wedge, chi=chi)
assert wc.dtype == float
# computed omega angles for reflections
omega1, omega2, valid = gv_general.g_to_k(g,
wavelength,
axis=[0, 0, -1],
pre=None,
post=wc)
assert omega1.dtype == float
# hum - isn't this wc-1 ?
cwT = gv_general.chiwedge(wedge=wedge, chi=chi).T
# k vectors, scattering in laboratory at angle omega1/2
k1 = gv_general.k_to_g(g, omega1, axis=[0, 0, 1], pre=cwT, post=None)
k2 = gv_general.k_to_g(g, omega2, axis=[0, 0, 1], pre=cwT, post=None)
assert k1.dtype == float
# Computed azimuth angles
#
# k[1,:] = -ds*c*sin(eta)
# ------ ------------- .... tan(eta) = -k1/k2
# k[2,:] = ds*c*cos(eta)
#
eta_one = np.degrees(np.arctan2(-k1[1, :], k1[2, :]))
eta_two = np.degrees(np.arctan2(-k2[1, :], k2[2, :]))
#
# We select the one matching the observed data
# FIXME - doesn't make sense to do this here
# pick the solution which is closest to matching in eta/omega
d1 = angmod(eta_one - etao)
d2 = angmod(eta_two - etao)
# Selecting which is the computed value for peaks
etac = np.where(abs(d1) < abs(d2), eta_one, eta_two)
omegac = np.where(abs(d1) < abs(d2), omega1, omega2)
if TESTING > 2:
err = abs(etac - etao)
for i in range(len(err)):
if err[i] < 1:
continue
print(i, eta_one[i], eta_two[i], omega1[i], omega2[i])
print("\t", etao[i], omega[i], etac[i], omegac[i])
# Two theta angles
mod_g = np.sqrt((g * g).sum(axis=0))
tthc = np.degrees(2 * np.arcsin(wavelength * mod_g / 2))
# Return computed values (no derivatives here)
return tthc, etac, omegac
testaxisang()
def anglediff(a1, a2):
return np.arctan2(np.sin(a1-a2), np.cos(a1-a2))
for wedge, chi in [(0.,0.),(-10.,0.), (11,-15), (0,6)]:
print "Wedge",wedge,"chi",chi
print "gve[0] gve[1] gve[2] om1py om2py om1af om2af omtrue"
gve = transform.compute_g_vectors( tth, eta, omega, wvln, wedge, chi )
gve = gve.T.copy()
post = gv_general.chiwedge( wedge=wedge, chi=chi )
posti = np.dot(gv_general.wedgemat(wedge), gv_general.chimat(chi)).T
# don't try to match this as it is wrong!!
# tth, eta, omega = transform.uncompute_g_vectors( hkl.T, wvln,
# wedge=wedge,
# chi = chi)
ppre = np.reshape(pre,(3,3))
ppost = np.reshape(post,(3,3))
omg1, omg2, valid = gv_general.g_to_k( gve.T, wvln, axis=axis, pre=ppre, post=ppost )
#print pre
#print posti.ravel()
#print axis