def test_find_omega_general_nowedge(self):
# generate random gvector
hkl = n.array([
round(n.random.rand() * 10 - 5),
round(n.random.rand() * 10 - 5),
round(n.random.rand() * 10 - 5)
])
ucell = n.array([
3.5 + n.random.rand(), 3.5 + n.random.rand(),
3.5 + n.random.rand(), 89.5 + n.random.rand(),
89.5 + n.random.rand(), 89.5 + n.random.rand()
])
B = tools.form_b_mat(ucell)
U = tools.euler_to_u(n.random.rand() * 2. * n.pi,
n.random.rand() * 2. * n.pi,
n.random.rand() * n.pi)
wavelength = 0.95 + n.random.rand() * 0.1
gvec = n.dot(U, n.dot(B, hkl))
tth = tools.tth(ucell, hkl, wavelength)
# calculate corresponding eta and Omega using tools.find_omega_general
(omega1,
eta1) = tools.find_omega_general(gvec * wavelength / (4. * n.pi), tth,
0, 0)
Om1 = []
for i in range(len(omega1)):
Om1.append(tools.form_omega_mat_general(omega1[i], 0, 0))
# calculate corresponding eta and Omega using tools.find_omega_wedge
omega2 = tools.find_omega(gvec, tth)
Om2 = []
for i in range(len(omega2)):
Om2.append(tools.form_omega_mat(omega2[i]))
#assert
for i in range(len(omega1)):
# print Om1[i]
# print Om2[i]
diff = n.abs(Om1[i] - Om2[i]).sum()
self.assertAlmostEqual(diff, 0, 9)
def make_image(self, grainno=None, refl=None):
from scipy import ndimage
if grainno == None:
do_grains = list(range(self.graindata.param['no_grains']))
else:
do_grains = [grainno]
# loop over grains
for grainno in do_grains:
gr_pos = n.array(self.graindata.param['pos_grains_%s' \
%(self.graindata.param['grain_list'][grainno])])
B = self.graindata.grain[grainno].B
SU = n.dot(self.graindata.S, self.graindata.grain[grainno].U)
if refl == None:
do_refs = list(range(len(self.graindata.grain[grainno].refs)))
else:
do_refs = [refl]
# loop over reflections for each grain
for nref in do_refs:
# exploit that the reflection list is sorted according to omega
print('\rDoing reflection %i of %i for grain %i of %i' %
(nref + 1, len(self.graindata.grain[grainno].refs),
grainno + 1, self.graindata.param['no_grains']),
end=' ')
sys.stdout.flush()
#print 'Doing reflection: %i' %nref
if self.graindata.param['odf_type'] == 3:
intensity = 1
else:
intensity = self.graindata.grain[grainno].refs[nref,
A_id['Int']]
hkl = n.array([
self.graindata.grain[grainno].refs[nref, A_id['h']],
self.graindata.grain[grainno].refs[nref, A_id['k']],
self.graindata.grain[grainno].refs[nref, A_id['l']]
])
Gc = n.dot(B, hkl)
for i in range(self.odf.shape[0]):
for j in range(self.odf.shape[1]):
for k in range(self.odf.shape[2]):
check_input.interrupt(self.killfile)
if self.odf[i, j, k] > self.odf_cut:
Gtmp = n.dot(self.Uodf[i, j, k], Gc)
Gw = n.dot(SU, Gtmp)
Glen = n.sqrt(n.dot(Gw, Gw))
tth = 2 * n.arcsin(Glen /
(2 * abs(self.graindata.K)))
costth = n.cos(tth)
Qw = Gw * self.graindata.param[
'wavelength'] / (4. * n.pi)
(Omega, eta) = tools.find_omega_general(
Qw, tth, self.wx, self.wy)
try:
minpos = n.argmin(
n.abs(Omega -
self.graindata.grain[grainno].
refs[nref, A_id['omega']]))
except:
print(Omega)
if len(Omega) == 0:
continue
omega = Omega[minpos]
# if omega not in rotation range continue to next step
if (self.graindata.param['omega_start']*n.pi/180) > omega or\
omega > (self.graindata.param['omega_end']*n.pi/180):
continue
Om = tools.form_omega_mat_general(
omega, self.wx, self.wy)
Gt = n.dot(Om, Gw)
# Calc crystal position at present omega
[tx, ty, tz] = n.dot(Om, gr_pos)
(dety, detz) = detector.det_coor(
Gt, costth,
self.graindata.param['wavelength'],
self.graindata.param['distance'],
self.graindata.param['y_size'],
self.graindata.param['z_size'],
self.graindata.param['dety_center'],
self.graindata.param['detz_center'],
self.graindata.R, tx, ty, tz)
if self.graindata.param['spatial'] != None:
# To match the coordinate system of the spline file
# SPLINE(i,j): i = detz; j = (dety_size-1)-dety
# Well at least if the spline file is for frelon2k
(x, y) = detector.detyz_to_xy(
[dety, detz],
self.graindata.param['o11'],
self.graindata.param['o12'],
self.graindata.param['o21'],
self.graindata.param['o22'],
self.graindata.param['dety_size'],
self.graindata.param['detz_size'])
# Do the spatial distortion
(xd, yd) = self.spatial.distort(x, y)
# transform coordinates back to dety,detz
(dety, detz) = detector.xy_to_detyz(
[xd, yd], self.graindata.param['o11'],
self.graindata.param['o12'],
self.graindata.param['o21'],
self.graindata.param['o22'],
self.graindata.param['dety_size'],
self.graindata.param['detz_size'])
if dety > -0.5 and dety <= self.graindata.param['dety_size']-0.5 and\
detz > -0.5 and detz <= self.graindata.param['detz_size']-0.5:
dety = int(round(dety))
detz = int(round(detz))
frame_no = int(n.floor((omega*180/n.pi-self.graindata.param['omega_start'])/\
self.graindata.param['omega_step']))
self.frames[frame_no][
dety, detz] = self.frames[frame_no][
dety,
detz] + intensity * self.odf[i, j,
k]
def find_refl(inp):
"""
From U, (x,y,z) and B determined for the far-field case
calculate the possible reflection on the near-field detector
output[grainno][reflno]=[h,k,l,omega,dety,detz,tth,eta]
"""
S = n.array([[1, 0, 0],[0, 1, 0],[0, 0, 1]])
R = tools.detect_tilt(inp.param['tilt_x'],
inp.param['tilt_y'],
inp.param['tilt_z'])
inp.possible = []
# if structure info is given use this
if inp.files['structure_file'] != None:
inp.param['structure_phase_0'] = inp.files['structure_file']
xtal_structure = reflections.open_structure(inp.param,0)
HKL = reflections.gen_miller(inp.param,0)
else:
inp.param['unit_cell_phase_0'] = inp.unit_cell
inp.param['sgno_phase_0'] = inp.fit['sgno']
HKL = reflections.gen_miller(inp.param,0)
for grainno in range(inp.no_grains):
inp.possible.append([])
if grainno+1 not in inp.fit['skip']:
B = tools.epsilon_to_b(n.array([inp.values['epsaa%s' %grainno],
inp.values['epsab%s' %grainno],
inp.values['epsac%s' %grainno],
inp.values['epsbb%s' %grainno],
inp.values['epsbc%s' %grainno],
inp.values['epscc%s' %grainno]]),
inp.unit_cell)
U = tools.rod_to_u([inp.rod[grainno][0]+inp.values['rodx%s' %grainno],
inp.rod[grainno][1]+inp.values['rody%s' %grainno],
inp.rod[grainno][2]+inp.values['rodz%s' %grainno]])
gr_pos = n.array([inp.values['x%s' %grainno],
inp.values['y%s' %grainno],
inp.values['z%s' %grainno]])
for hkl in HKL:
Gc = n.dot(B,hkl[0:3])
Gw = n.dot(S,n.dot(U,Gc))
tth = tools.tth2(Gw,inp.param['wavelength'])
# print hkl[0:3],tth*180./n.pi
costth = n.cos(tth)
(Omega, Eta) = tools.find_omega_general(inp.param['wavelength']/(4.*n.pi)*Gw,
tth,
inp.values['wx']*n.pi/180,
inp.values['wy']*n.pi/180)
if len(Omega) > 0:
for solution in range(len(Omega)):
omega = Omega[solution]
eta = Eta[solution]
for i in range(len(inp.fit['w_limit'])//2):
if (inp.fit['w_limit'][2*i]*n.pi/180) < omega and\
omega < (inp.fit['w_limit'][2*i+1]*n.pi/180):
# form Omega rotation matrix
Om = tools.form_omega_mat_general(omega,inp.values['wx']*n.pi/180,inp.values['wy']*n.pi/180)
Gt = n.dot(Om,Gw)
# Calc crystal position at present omega
[tx,ty,tz]= n.dot(Om,gr_pos)
# Calc detector coordinate for peak
(dety, detz) = detector.det_coor(Gt,costth,
inp.param['wavelength'],
inp.param['distance'],
inp.param['y_size'],
inp.param['z_size'],
inp.param['y_center'],
inp.param['z_center'],
R,tx,ty,tz)
#If peak within detector frame store it in possible
if (-0.5 < dety) and\
(dety < inp.fit['dety_size']-0.5) and\
(-0.5 < detz) and\
(detz < inp.fit['detz_size']-0.5):
inp.possible[grainno].append([hkl[0],
hkl[1],
hkl[2],
omega*180/n.pi,
dety,
detz,
tth,
eta])
def run(self):
spot_id = 0
# Generate orientations of the grains and loop over all grains
print('no of grains ', self.param['no_grains'])
for grainno in range(self.param['no_grains']):
A = []
U = self.param['U_grains_%s' % (self.param['grain_list'][grainno])]
if len(self.param['phase_list']) == 1:
phase = self.param['phase_list'][0]
else:
phase = self.param['phase_grains_%s' %
(self.param['grain_list'][grainno])]
unit_cell = self.param['unit_cell_phase_%i' % phase]
self.grain.append(variables.grain_cont(U))
gr_pos = n.array(self.param['pos_grains_%s' %
(self.param['grain_list'][grainno])])
gr_eps = n.array(self.param['eps_grains_%s' %
(self.param['grain_list'][grainno])])
# Calculate the B-matrix based on the strain tensor for each grain
B = tools.epsilon_to_b(gr_eps, unit_cell)
# add B matrix to grain container
self.grain[grainno].B = B
V = tools.cell_volume(unit_cell)
grain_vol = n.pi / 6 * self.param[
'size_grains_%s' % self.param['grain_list'][grainno]]**3
# print 'GRAIN NO: ',self.param['grain_list'][grainno]
# print 'GRAIN POSITION of grain ',self.param['grain_list'][grainno],': ',gr_pos
# print 'STRAIN TENSOR COMPONENTS (e11 e12 e13 e22 e23 e33) of grain ',self.param['grain_list'][grainno],':\n',gr_eps
# print 'U of grain ',self.param['grain_list'][grainno],':\n',U
nrefl = 0
# Calculate these values:
# totalnr, grainno, refno, hkl, omega, 2theta, eta, dety, detz
# For all reflections in Ahkl that fulfill omega_start < omega < omega_end.
# All angles in Grain are in degrees
for hkl in self.hkl[self.param['phase_list'].index(phase)]:
check_input.interrupt(self.killfile)
Gc = n.dot(B, hkl[0:3])
Gw = n.dot(self.S, n.dot(U, Gc))
tth = tools.tth2(Gw, self.param['wavelength'])
costth = n.cos(tth)
(Omega, Eta) = tools.find_omega_general(
Gw * self.param['wavelength'] / (4. * n.pi), tth, self.wx,
self.wy)
if len(Omega) > 0:
for solution in range(len(Omega)):
omega = Omega[solution]
eta = Eta[solution]
if (self.param['omega_start']*n.pi/180) < omega and\
omega < (self.param['omega_end']*n.pi/180):
# form Omega rotation matrix
Om = tools.form_omega_mat_general(
omega, self.wx, self.wy)
Gt = n.dot(Om, Gw)
# Calc crystal position at present omega and continue if this is outside the illuminated volume
[tx, ty, tz] = n.dot(Om, gr_pos)
if self.param['beam_width'] != None:
if n.abs(ty) > self.param['beam_width'] / 2.:
continue
# Calc detector coordinate for peak
(dety, detz) = detector.det_coor(
Gt, costth, self.param['wavelength'],
self.param['distance'], self.param['y_size'],
self.param['z_size'],
self.param['dety_center'],
self.param['detz_center'], self.R, tx, ty, tz)
#If shoebox extends outside detector exclude it
if (-0.5 > dety) or\
(dety > self.param['dety_size']-0.5) or\
(-0.5 > detz) or\
(detz > self.param['detz_size']-0.5):
continue
if self.param['spatial'] != None:
# To match the coordinate system of the spline file
(x, y) = detector.detyz_to_xy(
[dety, detz], self.param['o11'],
self.param['o12'], self.param['o21'],
self.param['o22'], self.param['dety_size'],
self.param['detz_size'])
# Do the spatial distortion
(xd, yd) = self.spatial.distort(x, y)
# transform coordinates back to dety,detz
(detyd, detzd) = detector.xy_to_detyz(
[xd, yd], self.param['o11'],
self.param['o12'], self.param['o21'],
self.param['o22'], self.param['dety_size'],
self.param['detz_size'])
else:
detyd = dety
detzd = detz
if self.param['beampol_apply'] == 1:
#Polarization factor (Kahn, J. Appl. Cryst. (1982) 15, 330-337.)
rho = n.pi / 2.0 + eta + self.param[
'beampol_direct'] * n.pi / 180.0
P = 0.5 * (1 + costth*costth -\
self.param['beampol_factor']*n.cos(2*rho)*n.sin(tth)**2)
else:
P = 1.0
#Lorentz factor
if self.param['lorentz_apply'] == 1:
if eta != 0:
L = 1 / (n.sin(tth) * abs(n.sin(eta)))
else:
L = n.inf
else:
L = 1.0
overlaps = 0 # set the number overlaps to zero
if self.param['intensity_const'] != 1:
intensity = int_intensity(
hkl[3], L, P, self.param['beamflux'],
self.param['wavelength'], V, grain_vol)
else:
intensity = hkl[3]
A.append([
self.param['grain_list'][grainno], nrefl,
spot_id, hkl[0], hkl[1], hkl[2], tth, omega,
eta, dety, detz, detyd, detzd, Gw[0], Gw[1],
Gw[2], L, P, hkl[3], intensity, overlaps
])
nrefl = nrefl + 1
spot_id = spot_id + 1
# print 'Length of Grain', len(self.grain[0].refl)
A = n.array(A)
if len(A) > 0:
# sort rows according to omega
A = A[n.argsort(A, 0)[:, A_id['omega']], :]
# Renumber the reflections
A[:, A_id['ref_id']] = n.arange(nrefl)
# Renumber the spot_id
A[:,
A_id['spot_id']] = n.arange(n.min(A[:, A_id['spot_id']]),
n.max(A[:, A_id['spot_id']]) + 1)
else:
A = n.zeros((0, len(A_id)))
# save reflection info in grain container
self.grain[grainno].refs = A
print('\rDone %3i grain(s) of %3i' %
(grainno + 1, self.param['no_grains']),
end=' ')
sys.stdout.flush()
print('\n')