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 assignpeaks( gr, pars, colfile, tol=None, omegatol=0.2 ):
labels = np.zeros( colfile.nrows )
cyf = cyfit.cyfit(pars)
cyf.setscfc( colfile.sc, colfile.fc )
hkl = np.zeros( cyf.XL.shape, np.float)
drlv = np.zeros( colfile.nrows, np.float)
kcalc = np.zeros( cyf.XL.shape, np.float)
r_omega = np.array(colfile.omega*np.pi/180.0,np.float)
cyf.hkl( colfile.sc, colfile.fc, r_omega, gr, hkl, kcalc )
# Make integer hkl
wripaca.ih_drlv( hkl, drlv )
# Now replace omegaobs by omegacalc where this is appropriate
pre = np.eye(3).ravel()
posti = np.dot(gv_general.wedgemat(pars.get('wedge')),
gv_general.chimat(pars.get('chi'))).T.ravel()
axis = np.array([0,0,-1],np.float)
ub = np.linalg.inv(gr.ubi)
gcalc = np.dot( ub, hkl.T ).T.copy()
#print hkl
romegacalc = np.zeros( r_omega.shape, np.float)
romegaerr = np.zeros( r_omega.shape, np.float)
wripaca.omegacalcclose(gcalc,
pre,
posti,
axis,
r_omega,
romegacalc,
romegaerr,
pars.get('wavelength'),
)
# OK, now we will accept anything within omegatol
if 0:
pylab.hist(romegaerr, bins=50)
pylab.figure()
pylab.plot(r_omega, romegaerr,",")
pylab.show()
r_omega = np.where( romegaerr < omegatol*np.pi/180., romegacalc, r_omega )
cyf.hkl( colfile.sc, colfile.fc, r_omega, gr, hkl, kcalc )
drlv_omegafree = drlv.copy()
wripaca.ih_drlv( hkl, drlv_omegafree )
m = drlv < tol
sc = colfile.sc[m]
fc = colfile.fc[m]
omegaobs = colfile.omega[m].astype(np.float)
omega = colfile.omega[m].astype(np.float)
hkl = hkl[m]
print "Got",m.sum(),"peaks",
if 0:
pylab.ion()
pylab.title("tol = %f"%(tol))
pylab.hist( drlv, bins=np.arange(0,0.05,0.001))
pylab.hist( drlv_omegafree, bins=np.arange(0,0.05,0.001))
pylab.show()
raw_input("OK?")
return dummycf( sc, fc, omega, omegaobs, hkl )
def omegacalc_ub( ubi, h, pars, romega):
pre = np.eye(3).ravel()
posti = np.dot(gv_general.wedgemat(pars.get('wedge')),
gv_general.chimat(pars.get('chi'))).T.ravel()
axis = np.array([0,0,-1],np.float)
ub = np.linalg.inv(ubi)
gcalc = np.dot( ub, h.T ).T.copy()
romegacalc = np.zeros( romega.shape, np.float)
romegaerr = np.zeros( romega.shape, np.float)
wripaca.omegacalcclose(gcalc,
pre,
posti,
axis,
romega,
romegacalc,
romegaerr,
pars.get('wavelength'),
)
return romegacalc
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
#print wvln
