def to_strain_and_angs(s_tilde, cell, nelm):
fun_val = []
ubs = s_tilde.reshape(nelm, 3, 3)
for i in range(nelm):
ubi = np.linalg.inv(ubs[i])
u, eps = tools.ubi_to_u_and_eps(ubi, cell)
euler = tools.u_to_euler(u)
fun_val.extend(eps)
fun_val.extend(list(euler))
return np.asarray(fun_val)
def _check_angles(self, angles):
'''Check consistency for euler_to_u() and u_to_euler(). I.e check that
the orientation matrix constructed for some set of angles is recovered
again when passing between the two functions.
'''
for phi1 in angles:
for PHI in angles:
for phi2 in angles:
U = tools.euler_to_u(phi1, PHI, phi2)
phi1_new, PHI_new, phi2_new = tools.u_to_euler(U)
U_new = tools.euler_to_u(phi1_new, PHI_new, phi2_new)
maxdiff = n.max(n.abs(U - U_new))
self.assertTrue(maxdiff < 1e-8)
self.assertTrue(0 <= phi1_new <= 2 * n.pi)
self.assertTrue(0 <= PHI_new <= 2 * n.pi)
self.assertTrue(0 <= phi2_new <= 2 * n.pi)
def run_pcr(self, cif_file, grain_mask, flt, gr, number_y_scans, ymin,
ystep):
no_voxels = sum(grain_mask[grain_mask == 1])
unit_cell = self.field_converter.extract_cell(self.params)
UBI = gr.ubi.copy()
cell = tools.ubi_to_cell(UBI)
U, strain = tools.ubi_to_u_and_eps(UBI, unit_cell)
euler = tools.u_to_euler(U)
average = np.concatenate((strain, euler), axis=None)
initial_guess = np.concatenate((average, average), axis=None)
for i in range(no_voxels - 2):
initial_guess = np.concatenate((initial_guess, average), axis=None)
th_min, th_max = setup_grain.get_theta_bounds(flt, gr)
param = setup_grain.setup_experiment(self.params, cif_file, no_voxels,
ystep, th_min, th_max)
measured_data = setup_grain.get_measured_data(gr, flt, number_y_scans,
ymin, ystep, param)
hkl = setup_grain.get_hkls(param, flt, gr)
voxel_positions, C, constraint = setup_grain.get_positions(
grain_mask, ystep)
voxel_data = find_refl_func.find_refl_func(param, hkl, voxel_positions,
measured_data, unit_cell,
initial_guess, ymin,
number_y_scans, C,
constraint)
bounds_low, bounds_high = setup_grain.get_bounds_strain(initial_guess)
solution = voxel_data.steepest_descent(bounds_low, bounds_high,
initial_guess)
voxels_as_grain_objects = setup_grain.map_solution_to_voxels(
solution, grain_mask, no_voxels, voxel_data, var_choice='strain')
return voxels_as_grain_objects
def write_grains(param):
# Save the generated grain parameters, pos, U and eps
#
# INPUT: The parameter set from the input file and the grain generator
# OUTPUT: grainno x y z phi1 PHI phi2 U11 U12 U13 U21 U22 U23 U31 U32 U33 eps11 eps12 eps13 eps22 eps23 eps33
#
# Jette Oddershede, Risoe DTU, March 31 2008
#
filename = '%s/%s.gff' % (param['direc'], param['stem'])
f = open(filename, 'w')
# format = "%d "*1 + "%f "*1 + "%e"*1 + "%f"*18 + "\n"
format = "%d " * 1 + "%d " * 1 + "%f " * 1 + "%e " * 1 + "%f " * 6 + "%0.12f " * 9 + "%0.12f " * 9 + "%e " * 6 + "\n"
out = "# grain_id phase_id grainsize grainvolume x y z phi1 PHI phi2 U11 U12 U13 U21 U22 U23 U31 U32 U33 UBI11 UBI12 UBI13 UBI21 UBI22 UBI23 UBI31 UBI32 UBI33 eps11 eps12 eps13 eps22 eps23 eps33 \n"
f.write(out)
for i in range(param['no_grains']):
euler = 180 / n.pi * tools.u_to_euler(param['U_grains_%s' %
(param['grain_list'][i])])
if len(param['phase_list']) == 1:
phase = param['phase_list'][0]
else:
phase = param['phase_grains_%s' % (param['grain_list'][i])]
b = tools.epsilon_to_b(
param['eps_grains_%s' % (param['grain_list'][i])],
param['unit_cell_phase_%i' % phase])
u = param['U_grains_%s' % (param['grain_list'][i])]
ubi = n.linalg.inv(n.dot(u, b)) * 2 * n.pi
out = format % (
param['grain_list'][i],
phase,
param['size_grains_%s' % (param['grain_list'][i])],
n.pi / 6 * (param['size_grains_%s' %
(param['grain_list'][i])])**3.,
param['pos_grains_%s' % (param['grain_list'][i])][0],
param['pos_grains_%s' % (param['grain_list'][i])][1],
param['pos_grains_%s' % (param['grain_list'][i])][2],
euler[0],
euler[1],
euler[2],
param['U_grains_%s' % (param['grain_list'][i])][0, 0],
param['U_grains_%s' % (param['grain_list'][i])][0, 1],
param['U_grains_%s' % (param['grain_list'][i])][0, 2],
param['U_grains_%s' % (param['grain_list'][i])][1, 0],
param['U_grains_%s' % (param['grain_list'][i])][1, 1],
param['U_grains_%s' % (param['grain_list'][i])][1, 2],
param['U_grains_%s' % (param['grain_list'][i])][2, 0],
param['U_grains_%s' % (param['grain_list'][i])][2, 1],
param['U_grains_%s' % (param['grain_list'][i])][2, 2],
ubi[0, 0],
ubi[0, 1],
ubi[0, 2],
ubi[1, 0],
ubi[1, 1],
ubi[1, 2],
ubi[2, 0],
ubi[2, 1],
ubi[2, 2],
param['eps_grains_%s' % (param['grain_list'][i])][0],
param['eps_grains_%s' % (param['grain_list'][i])][1],
param['eps_grains_%s' % (param['grain_list'][i])][2],
param['eps_grains_%s' % (param['grain_list'][i])][3],
param['eps_grains_%s' % (param['grain_list'][i])][4],
param['eps_grains_%s' % (param['grain_list'][i])][5],
)
f.write(out)
f.close()
def write_voxels(param):
'''
Save the generated voxel parameters, pos, U and eps
INPUT: The parameter set from the input file and the voxel generator
OUTPUT: voxelno x y z phi1 PHI phi2 U11 U12 U13 U21 U22 U23 U31 U32 U33 eps11 eps12 eps13 eps22 eps23 eps33
'''
filename = '%s/%s.gff' %(param['direc'],param['stem'])
with open(filename,'w') as f:
# format = "%d "*1 + "%f "*1 + "%e"*1 + "%f"*18 + "\n"
format = "%d "*1 + "%d "*1 + "%f "*1 + "%e "*1 + "%f "*6 + "%0.12f "*9 + "%0.12f "*9 + "%e "*6 +"\n"
out = "# voxel_id phase_id voxelsize voxelvolume x y z phi1 PHI phi2 U11 U12 U13 U21 U22 U23 U31 U32 U33 UBI11 UBI12 UBI13 UBI21 UBI22 UBI23 UBI31 UBI32 UBI33 eps11 eps12 eps13 eps22 eps23 eps33 \n"
f.write(out)
for i in range(param['no_voxels']):
euler = 180/n.pi*tools.u_to_euler(param['U_voxels_%s' %(param['voxel_list'][i])])
if len(param['phase_list']) == 1:
phase = param['phase_list'][0]
else:
phase = param['phase_voxels_%s' %(param['voxel_list'][i])]
b = tools.epsilon_to_b(param['eps_voxels_%s' %(param['voxel_list'][i])],
param['unit_cell_phase_%i' %phase ])
u = param['U_voxels_%s' %(param['voxel_list'][i])]
ubi = n.linalg.inv(n.dot(u,b))*2*n.pi
out = format %(param['voxel_list'][i],
phase,
param['size_voxels_%s' %(param['voxel_list'][i])],
n.pi/6*(param['size_voxels_%s' %(param['voxel_list'][i])])**3.,
param['pos_voxels_%s' %(param['voxel_list'][i])][0],
param['pos_voxels_%s' %(param['voxel_list'][i])][1],
param['pos_voxels_%s' %(param['voxel_list'][i])][2],
euler[0],
euler[1],
euler[2],
param['U_voxels_%s' %(param['voxel_list'][i])][0,0],
param['U_voxels_%s' %(param['voxel_list'][i])][0,1],
param['U_voxels_%s' %(param['voxel_list'][i])][0,2],
param['U_voxels_%s' %(param['voxel_list'][i])][1,0],
param['U_voxels_%s' %(param['voxel_list'][i])][1,1],
param['U_voxels_%s' %(param['voxel_list'][i])][1,2],
param['U_voxels_%s' %(param['voxel_list'][i])][2,0],
param['U_voxels_%s' %(param['voxel_list'][i])][2,1],
param['U_voxels_%s' %(param['voxel_list'][i])][2,2],
ubi[0,0],
ubi[0,1],
ubi[0,2],
ubi[1,0],
ubi[1,1],
ubi[1,2],
ubi[2,0],
ubi[2,1],
ubi[2,2],
param['eps_voxels_%s' %(param['voxel_list'][i])][0],
param['eps_voxels_%s' %(param['voxel_list'][i])][1],
param['eps_voxels_%s' %(param['voxel_list'][i])][2],
param['eps_voxels_%s' %(param['voxel_list'][i])][3],
param['eps_voxels_%s' %(param['voxel_list'][i])][4],
param['eps_voxels_%s' %(param['voxel_list'][i])][5],
)
f.write(out)