def write_ini(param, hkl):
"""
Write ini file for grainspotter, see
http://fable.wiki.sourceforge.net/grainspotter
Henning Osholm Sorensen, RisoeDTU, 2008.
"""
for phase in param['phase_list']:
out = '! input file for GrainSpotter made by PolyXSim\n'
if param['no_phases'] > 1:
filename = '%s/%s_phase_%i.ini' % (param['direc'], param['stem'],
phase)
out = out + 'filespecs %s/%s_phase_%i.gve %s/%s_phase_%i.log\n' % (
param['direc'], param['stem'], phase, param['direc'],
param['stem'], phase)
else:
filename = '%s/%s.ini' % (param['direc'], param['stem'])
out = out + 'filespecs %s/%s.gve %s/%s.log\n' % (
param['direc'], param['stem'], param['direc'], param['stem'])
unit_cell = param['unit_cell_phase_%i' % phase]
thkl = hkl[param['phase_list'].index(phase)].copy()
ds = n.zeros((thkl.shape[0], 1))
for i in range(thkl.shape[0]):
ds[i] = 2 * tools.sintl(unit_cell, thkl[i, 0:3])
ds.sort()
ds = ds.round(9)
ds = n.unique(ds)
families = len(ds)
Nhkls = n.min([families, 8])
extra_hkls = 4
if families - Nhkls < extra_hkls:
tth_max = 2 * param['theta_max']
else:
ds_max = ds[Nhkls + extra_hkls - 1] + 0.001
tth_max = 2 * n.arcsin(
ds_max * param['wavelength'] / 2.) * 180. / n.pi
ds_min = ds[0] - 0.001
if ds_min < 0.0:
ds_min = 0.
tth_min = 2 * n.arcsin(ds_min * param['wavelength'] / 2.) * 180. / n.pi
out = out + 'spacegroup %i\n' % param['sgno_phase_%i' % phase]
out = out + 'etarange %f %f\n' % (0.0, 360.0)
out = out + 'domega %f\n' % param['omega_step']
out = out + 'omegarange %f %f\n' % (param['omega_start'],
param['omega_end'])
out = out + 'cuts %i %f %f\n' % (8, 0.6, 0.75)
out = out + 'eulerstep %f\n' % (5.0)
out = out + 'uncertainties %f %f %f\n' % (.05, 0.5, 1.0)
out = out + 'nsigmas %f\n' % (2.0)
out = out + 'Nhkls_in_indexing %i\n' % (Nhkls)
out = out + 'tthrange %f %f\n' % (tth_min, tth_max)
out = out + 'minfracg %f\n' % (0.95)
f = open(filename, 'w')
f.write(out)
def StructureFactor(hkl, ucell, sgname, atoms, disper=None):
"""
Calculation of the structure factor of reflection hkl
[Freal Fimg] = StructureFactor(hkl,unit_cell,sg,atoms)
INPUT : hkl = [h, k, l]
unit_cell = [a, b, c, alpha, beta, gamma]
sgname: space group name (e.g. 'P 21/c')
atoms: structural parameters (as an object)
OUTPUT: The real and imaginary parts of the the structure factor
Henning Osholm Sorensen, June 23, 2006.
Translated to python code April 8, 2008
"""
mysg = sg.sg(sgname=sgname)
stl = tools.sintl(ucell, hkl)
noatoms = len(atoms)
Freal = 0.0
Fimg = 0.0
for i in range(noatoms):
#Check whether isotrop or anisotropic displacements
if atoms[i].adp_type == 'Uiso':
U = atoms[i].adp
expij = n.exp(-8 * n.pi**2 * U * stl**2)
elif atoms[i].adp_type == 'Uani':
# transform Uij to betaij
betaij = Uij2betaij(atoms[i].adp, ucell)
else:
expij = 1
atoms[i].adp = 'Uiso'
#logging.error("wrong no of elements in atomlist")
# Atomic form factors
f = FormFactor(atoms[i].atomtype, stl)
if disper == None or disper[atoms[i].atomtype] == None:
fp = 0.0
fpp = 0.0
else:
fp = disper[atoms[i].atomtype][0]
fpp = disper[atoms[i].atomtype][1]
for j in range(mysg.nsymop):
# atomic displacement factor
if atoms[i].adp_type == 'Uani':
betaijrot = n.dot(mysg.rot[j], n.dot(betaij, mysg.rot[j]))
expij = n.exp(-n.dot(hkl, n.dot(betaijrot, hkl)))
# exponent for phase factor
r = n.dot(mysg.rot[j], atoms[i].pos) + mysg.trans[j]
exponent = 2 * n.pi * n.dot(hkl, r)
#forming the real and imaginary parts of F
s = n.sin(exponent)
c = n.cos(exponent)
site_pop = atoms[i].occ * atoms[i].symmulti / mysg.nsymop
Freal = Freal + expij * (c * (f + fp) - s * fpp) * site_pop
Fimg = Fimg + expij * (s * (f + fp) + c * fpp) * site_pop
return [Freal, Fimg]
def write_gve(param, grain, hkl):
"""
Write gvector (gve) file, for format see
http://fable.wiki.sourceforge.net/imaged11+-+file+formats
Henning Osholm Sorensen, RisoeDTU, 2008.
python translation: Jette Oddershede, Risoe DTU, March 31 2008
changed October 1, 2008 to new .gve format including detector.par and [xl,yl,zl]
"""
A = grain[0].refs
for grainno in range(1, param['no_grains']):
A = n.concatenate((A, grain[grainno].refs))
nrefl = A.shape[0]
# from detector.par
(z_center, y_center) = detector.detyz_to_xy(
[param['dety_center'], param['detz_center']], param['o11'],
param['o12'], param['o21'], param['o22'], param['dety_size'],
param['detz_size'])
dout = "# chi 0.0\n"
dout = dout + "# distance %f\n" % (param['distance'] * 1000.)
dout = dout + "# fit_tolerance 0.5\n"
dout = dout + "# o11 %i\n" % param['o11']
dout = dout + "# o12 %i\n" % param['o12']
dout = dout + "# o21 %i\n" % param['o21']
dout = dout + "# o22 %i\n" % param['o22']
dout = dout + "# omegasign %f\n" % param['omega_sign']
dout = dout + "# t_x 0\n"
dout = dout + "# t_y 0\n"
dout = dout + "# t_z 0\n"
dout = dout + "# tilt_x %f\n" % param['tilt_x']
dout = dout + "# tilt_y %f\n" % param['tilt_y']
dout = dout + "# tilt_z %f\n" % param['tilt_z']
dout = dout + "# y_center %f\n" % y_center
dout = dout + "# y_size %f\n" % (param['y_size'] * 1000.)
dout = dout + "# z_center %f\n" % z_center
dout = dout + "# z_size %f\n" % (param['z_size'] * 1000.)
for phase in param['phase_list']:
if param['no_phases'] > 1:
filename = '%s/%s_phase_%i.gve' % (param['direc'], param['stem'],
phase)
else:
filename = '%s/%s.gve' % (param['direc'], param['stem'])
f = open(filename, 'w')
lattice = param['sgname_phase_%i' % phase][0]
format = "%f " * 6 + "%s " * 1 + "\n"
unit_cell = param['unit_cell_phase_%i' % phase]
out = format % (unit_cell[0], unit_cell[1], unit_cell[2], unit_cell[3],
unit_cell[4], unit_cell[5], lattice)
out = out + "# wavelength = %s\n" % (param['wavelength'])
out = out + "# wedge = %f\n" % (param['wedge'])
out = out + "# axis = 0.000 0.0000 1.0000\n"
# insert detector.par as comment
out = out + "# cell__a %s\n" % unit_cell[0]
out = out + "# cell__b %s\n" % unit_cell[1]
out = out + "# cell__c %s\n" % unit_cell[2]
out = out + "# cell_alpha %s\n" % unit_cell[3]
out = out + "# cell_beta %s\n" % unit_cell[4]
out = out + "# cell_gamma %s\n" % unit_cell[5]
out = out + "# cell_lattice_[P,A,B,C,I,F,R] %s\n" % param[
'sgname_phase_%i' % phase][0]
out = out + dout
# continue with gve format
out = out + "# ds h k l\n"
f.write(out)
thkl = hkl[param['phase_list'].index(phase)].copy()
ds = n.zeros((thkl.shape[0], 1))
for i in range(thkl.shape[0]):
ds[i] = 2 * tools.sintl(unit_cell, thkl[i, 0:3])
#Add ds values to the thkl array
thkl = n.concatenate((thkl, ds), 1)
# sort rows according to ds, descending
thkl = thkl[n.argsort(thkl, 0)[:, 4], :]
# Output format
format = "%f " * 1 + "%d " * 3 + "\n"
for i in range(thkl.shape[0]):
out = format % (thkl[i, 4], thkl[i, 0], thkl[i, 1], thkl[i, 2])
f.write(out)
R_tilt = tools.detect_tilt(param['tilt_x'], param['tilt_y'],
param['tilt_z'])
out = "# xr yr zr xc yc ds eta omega spot3d_id xl yl zl\n"
f.write(out)
format = "%f " * 8 + "%i " * 1 + "%f " * 3 + "\n"
for i in range(nrefl):
(sc, fc) = detector.detyz_to_xy(
[A[i, A_id['dety']], A[i, A_id['detz']]], param['o11'],
param['o12'], param['o21'], param['o22'], param['dety_size'],
param['detz_size'])
[xl, yl,
zl] = detector.detector_to_lab(A[i, A_id['dety']],
A[i,
A_id['detz']], param['distance'],
param['y_size'], param['z_size'],
param['dety_center'],
param['detz_center'], R_tilt)
out = format % (
A[i, A_id['gv1']] / (2 * n.pi),
A[i, A_id['gv2']] / (2 * n.pi),
A[i, A_id['gv3']] / (2 * n.pi),
sc, #A[i,A_id['detz']],
fc, #param['dety_size']-A[i,A_id['dety']],
(2 * n.sin(.5 * A[i, A_id['tth']]) / param['wavelength']),
A[i, A_id['eta']] * 180 / n.pi,
A[i, A_id['omega']] * 180 / n.pi,
A[i, A_id['spot_id']],
xl * 1000.,
yl * 1000.,
zl * 1000.)
f.write(out)
f.close()
def write_delta_gve(param,voxel,hkl):
if not memory_safety_check(param):
return
"""
Write gvector (gve) file, for format see
http://fable.wiki.sourceforge.net/imaged11+-+file+formats
python translation: March 31 2008
changed October 1, 2008 to new .gve format including detector.par and [xl,yl,zl]
"""
# from detector.par
(z_center, y_center) = detector.detyz_to_xy([param['dety_center'],param['detz_center']],
param['o11'],
param['o12'],
param['o21'],
param['o22'],
param['dety_size'],
param['detz_size'])
dout = "# chi 0.0\n"
dout = dout + "# distance %f\n" %(param['distance']*1000.)
dout = dout + "# fit_tolerance 0.5\n"
dout = dout + "# o11 %i\n" %param['o11']
dout = dout + "# o12 %i\n" %param['o12']
dout = dout + "# o21 %i\n" %param['o21']
dout = dout + "# o22 %i\n" %param['o22']
dout = dout + "# omegasign %f\n" %param['omega_sign']
dout = dout + "# t_x 0\n"
dout = dout + "# t_y 0\n"
dout = dout + "# t_z 0\n"
dout = dout + "# tilt_x %f\n" %param['tilt_x']
dout = dout + "# tilt_y %f\n" %param['tilt_y']
dout = dout + "# tilt_z %f\n" %param['tilt_z']
dout = dout + "# y_center %f\n" %y_center
dout = dout + "# y_size %f\n" %(param['y_size']*1000.)
dout = dout + "# z_center %f\n" %z_center
dout = dout + "# z_size %f\n" %(param['z_size']*1000.)
for phase in param['phase_list']:
if param['no_phases'] > 1:
filename = '%s/%s%s_phase_%i.gve' %(param['direc'],'delta_peaks_',param['stem'],phase)
else:
filename = '%s/%s%s.gve' %(param['direc'],'delta_peaks_',param['stem'])
with open(filename,'w') as f:
lattice = param['sgname_phase_%i' %phase][0]
format = "%f "*6 + "%s "*1 +"\n"
unit_cell = param['unit_cell_phase_%i' %phase]
out = format %(unit_cell[0],unit_cell[1],unit_cell[2],
unit_cell[3],unit_cell[4],unit_cell[5],
lattice)
out = out + "# wavelength = %s\n" %(param['wavelength'])
out = out + "# wedge = %f\n" %(param['wedge'])
out = out + "# axis = 0.000 0.0000 1.0000\n"
# insert detector.par as comment
out = out + "# cell__a %s\n" %unit_cell[0]
out = out + "# cell__b %s\n" %unit_cell[1]
out = out + "# cell__c %s\n" %unit_cell[2]
out = out + "# cell_alpha %s\n" %unit_cell[3]
out = out + "# cell_beta %s\n" %unit_cell[4]
out = out + "# cell_gamma %s\n" %unit_cell[5]
out = out + "# cell_lattice_[P,A,B,C,I,F,R] %s\n" %param['sgname_phase_%i' %phase][0]
out = out + dout
# continue with gve format
out = out +"# ds h k l\n"
f.write(out)
thkl = hkl[param['phase_list'].index(phase)].copy()
ds = n.zeros((thkl.shape[0],1))
for i in range(thkl.shape[0]):
ds[i] = 2*tools.sintl(unit_cell,thkl[i,0:3])
#Add ds values to the thkl array
thkl = n.concatenate((thkl,ds),1)
# sort rows according to ds, descending
thkl = thkl[n.argsort(thkl,0)[:,4],:]
# Output format
format = "%f "*1 + "%d "*3 +"\n"
for i in range(thkl.shape[0]):
out = format %(thkl[i,4],
thkl[i,0],
thkl[i,1],
thkl[i,2]
)
f.write(out)
R_tilt = tools.detect_tilt(param['tilt_x'],param['tilt_y'],param['tilt_z'])
out = "# xr yr zr xc yc ds eta omega spot3d_id xl yl zl\n"
f.write(out)
# TODO: if we are writing huge files we need to be a little
# bit tender with the ram usage. Which is still kinda stupid
# as whoever tries to read such a file to RAM will get a
# nasty suprise. Perhaps a better solution is to write several .flt files
# Anyway, this should not be a problem once peakmerging is implemented
if param['no_voxels']>100:
collected_voxels = 0
ranges = []
while( True ):
low_line = collected_voxels
top_line = collected_voxels + 100
if top_line < param['no_voxels']:
ranges.append([low_line,top_line])
else:
ranges.append([low_line,param['no_voxels']])
break
collected_voxels = top_line
else:
ranges = [[0,param['no_voxels']]]
#Local implementation of detecter.detyz_to_xy() for speed
#--------------------------------------------------------
if abs(param['o11']) == 1:
if (abs(param['o22']) != 1) or (param['o12'] != 0) or (param['o21'] != 0):
raise ValueError('detector orientation makes no sense 1')
elif abs(param['o12']) == 1:
if abs(param['o21']) != 1 or (param['o11'] != 0) or (param['o22'] != 0):
raise ValueError('detector orientation makes no sense 2')
else:
raise ValueError('detector orientation makes no sense 3')
omat = n.array([[param['o11'], param['o12']],
[param['o21'], param['o22']]])
omat = n.linalg.inv(omat)
det_size = n.array([param['detz_size']-1,
param['dety_size']-1])
term2 = n.clip(n.dot(omat, det_size),-n.max(det_size), 0)
def detyz_to_xy(coor,omat,det_size,term2):
coor = n.array([coor[1], coor[0]])
coor = n.dot(omat, coor) - term2
return coor
#-------------------------------------------------------------
format = "%f "*8 + "%i "*1+ "%f "*3+"\n"
nrefl = 0
for ran in ranges:
out=""
A = voxel[ ran[0] ].refs
for voxelno in range(ran[0]+1,ran[1]):
A = n.concatenate((A,voxel[voxelno].refs))
for i in range(A.shape[0]):
(sc, fc) = detector.detyz_to_xy([A[i,A_id['dety']],A[i,A_id['detz']]],
param['o11'],
param['o12'],
param['o21'],
param['o22'],
param['dety_size'],
param['detz_size'])
[xl,yl,zl] = detector.detector_to_lab(A[i,A_id['dety']],A[i,A_id['detz']],
param['distance'],
param['y_size'],param['z_size'],
param['dety_center'],param['detz_center'],
R_tilt)
out = out + (format %(A[i,A_id['gv1']]/(2*n.pi),
A[i,A_id['gv2']]/(2*n.pi),
A[i,A_id['gv3']]/(2*n.pi),
sc,#A[i,A_id['detz']],
fc,#param['dety_size']-A[i,A_id['dety']],
(2*n.sin(.5*A[i,A_id['tth']])/param['wavelength']),
A[i,A_id['eta']]*180/n.pi,
A[i,A_id['omega']]*180/n.pi,
A[i,A_id['spot_id']],
xl*1000.,
yl*1000.,
zl*1000.
) )
f.write(out)
nrefl = nrefl + A.shape[0]
print('\rFinished %3i of %3i voxels. Written %3i reflections to file' %(ran[1],param['no_voxels'],nrefl), end=' ')
sys.stdout.flush()
print("\n")