def make_index_table(prefix='./v01-') :
from algos.core.GlobalUtils import str_tstamp
fname = '%s**t-cxif5315-r0169-%s.txt' % (prefix, str_tstamp())
fout = open(fname,'w')
fout.write('# file name: %s\n' % fname)
#------------------------------
# Photon energy
Egamma_eV = 6003.1936 # eV SIOC:SYS0:ML00:AO541
wavelen_nm = wavelength_nm_from_energy_ev(Egamma_eV) # nm
evald_rad = wave_vector_value(Egamma_eV) # 1/A
#-------
sigma_ql = 0.002 * evald_rad
sigma_qt = 0.002 * evald_rad
#-------
rec = '\n# photon energy = %.4f eV' % (Egamma_eV)\
+ '\n# wavelength = %.4f A' % (wavelen_nm*10)\
+ '\n# wave number/Evald radius k = 1/lambda = %.6f 1/A' % (evald_rad)\
+ '\n# sigma_ql = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_ql)\
+ '\n# sigma_qt = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_qt)\
+ '<sample-to-detector distance> = k*100um/100mm)'\
+ '\n# 3*sigma_ql = %.6f 1/A\n' % (3*sigma_ql)\
+ '\n# 3*sigma_qt = %.6f 1/A\n' % (3*sigma_qt)
print rec
fout.write(rec)
#------------------------------
# Lattice parameters
# from previous analysis note:
#a, b, c = 18.36, 26.65, 4.81 # Angstrom
#alpha, beta, gamma = 90, 90, 77.17 # 180 - 102.83 degree
a= 18.55 # Angstrom
b, c = 1.466*a, 0.262*a # Angstrom
alpha, beta, gamma = 90, 90, 78.47 # 180 - 101.53 degree
hmax, kmax, lmax = 4, 6, 0 # size of lattice to consider
a1, a2, a3 = triclinic_primitive_vectors(a, b, c, alpha, beta, gamma)
b1, b2, b3 = reciprocal_from_bravias(a1, a2, a3)
msg1 = '\n# Triclinic crystal cell parameters:'\
+ '\n# a = %.2f A\n# b = %.2f A\n# c = %.2f A' % (a, b, c)\
+ '\n# alpha = %.2f deg\n# beta = %.2f deg\n# gamma = %.2f deg' % (alpha, beta, gamma)
msg2 = '\n# 3-d space primitive vectors:\n# a1 = %s\n# a2 = %s\n# a3 = %s' %\
(str(a1), str(a2), str(a3))
msg3 = '\n# reciprocal space primitive vectors:\n# b1 = %s\n# b2 = %s\n# b3 = %s' %\
(str(b1), str(b2), str(b3))
rec = '%s\n%s\n%s\n' % (msg1, msg2, msg3)
print rec
fout.write(rec)
fout.write('\n# %s\n\n' % (89*'_'))
#for line in triclinic_primitive_vectors.__doc__.split('\n') : fout.write('\n# %s' % line)
test_lattice (b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, 1, cdtype=np.float32)
#------------------------------
#return
#------------------------------
# binning for look-up table and plots
# bin parameters for q in units of k = Evald's sphere radius [1/A]
bpq = BinPars((-0.25, 0.25), 1000, vtype=np.float32, endpoint=False)
# bin parameters for omega [degree] - fiber rotation angle around axis
bpomega = BinPars((0., 180.), 360, vtype=np.float32, endpoint=False)
# bin parameters for beta [degree] - fiber axis tilt angle
#bpbeta = BinPars((15., 195.), 2, vtype=np.float32, endpoint=True)
#bpbeta = BinPars((15., 15.), 1, vtype=np.float32, endpoint=False)
#bpbeta = BinPars((5., 25.), 2, vtype=np.float32, endpoint=True)
bpbeta = BinPars((0., 50.), 11, vtype=np.float32, endpoint=True)
bpbeta2 = BinPars((180., 230.), 11, vtype=np.float32, endpoint=True)
str_beta = 'for-beta:%s' % (bpbeta.strrange)
print '\n%s\nIndexing lookup table\n' % (91*'_')
lut = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32, evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega, bpbeta)
lut2 = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32, evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega, bpbeta2)
fout.close()
print '\nIndexing lookup table is saved in the file: %s' % fname
#------------------------------
# produce and save plots
import algos.graph.GlobalGraphics as gg
img = lut # or lut2
img = lut + lut2
img_range = (bpq.vmin, bpq.vmax, bpomega.vmax, bpomega.vmin)
axim = gg.plotImageLarge(lut, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Non-symmetrized for beta', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Symmetrized for beta (beta, beta+pi)', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-sym-%s.png' % (prefix, str_beta), pbits=1)
arrhi = np.sum(img,0)
fighi, axhi, hi = gg.hist1d(bpq.binedges, bins=bpq.nbins-1, amp_range=(bpq.vmin, bpq.vmax), weights=arrhi,\
color='b', show_stat=True, log=False,\
figsize=(15,5), axwin=(0.05, 0.12, 0.85, 0.80),\
title=None, xlabel='$q_{H}$ ($1/\AA$)', ylabel='Intensity', titwin=None)
gg.show()
gg.save_fig(fighi, '%splot-his-prob-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
qh_weight = zip(bpq.bincenters, arrhi)
fname = '%sarr-qh-weight-%s.npy' % (prefix, str_beta)
print 'Save qh:weigt array in file %s' % fname
np.save(fname, qh_weight)
def make_index_table(prefix='./v01-'):
from algos.core.GlobalUtils import str_tstamp
fname = '%s**t-cxif5315-r0169-%s.txt' % (prefix, str_tstamp())
fout = open(fname, 'w')
fout.write('# file name: %s\n' % fname)
#------------------------------
# Photon energy
Egamma_eV = 6003.1936 # eV SIOC:SYS0:ML00:AO541
wavelen_nm = wavelength_nm_from_energy_ev(Egamma_eV) # nm
evald_rad = wave_vector_value(Egamma_eV) # 1/A
#-------
sigma_ql = 0.002 * evald_rad
sigma_qt = 0.002 * evald_rad
#-------
rec = '\n# photon energy = %.4f eV' % (Egamma_eV)\
+ '\n# wavelength = %.4f A' % (wavelen_nm*10)\
+ '\n# wave number/Evald radius k = 1/lambda = %.6f 1/A' % (evald_rad)\
+ '\n# sigma_ql = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_ql)\
+ '\n# sigma_qt = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_qt)\
+ '<sample-to-detector distance> = k*100um/100mm)'\
+ '\n# 3*sigma_ql = %.6f 1/A\n' % (3*sigma_ql)\
+ '\n# 3*sigma_qt = %.6f 1/A\n' % (3*sigma_qt)
print rec
fout.write(rec)
#------------------------------
# Lattice parameters
# from previous analysis note:
#a, b, c = 18.36, 26.65, 4.81 # Angstrom
#alpha, beta, gamma = 90, 90, 77.17 # 180 - 102.83 degree
a = 18.55 # Angstrom
b, c = 1.466 * a, 0.262 * a # Angstrom
alpha, beta, gamma = 90, 90, 78.47 # 180 - 101.53 degree
hmax, kmax, lmax = 4, 6, 0 # size of lattice to consider
a1, a2, a3 = triclinic_primitive_vectors(a, b, c, alpha, beta, gamma)
b1, b2, b3 = reciprocal_from_bravias(a1, a2, a3)
msg1 = '\n# Triclinic crystal cell parameters:'\
+ '\n# a = %.2f A\n# b = %.2f A\n# c = %.2f A' % (a, b, c)\
+ '\n# alpha = %.2f deg\n# beta = %.2f deg\n# gamma = %.2f deg' % (alpha, beta, gamma)
msg2 = '\n# 3-d space primitive vectors:\n# a1 = %s\n# a2 = %s\n# a3 = %s' %\
(str(a1), str(a2), str(a3))
msg3 = '\n# reciprocal space primitive vectors:\n# b1 = %s\n# b2 = %s\n# b3 = %s' %\
(str(b1), str(b2), str(b3))
rec = '%s\n%s\n%s\n' % (msg1, msg2, msg3)
print rec
fout.write(rec)
fout.write('\n# %s\n\n' % (89 * '_'))
#for line in triclinic_primitive_vectors.__doc__.split('\n') : fout.write('\n# %s' % line)
test_lattice(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, 1, cdtype=np.float32)
#------------------------------
#return
#------------------------------
# binning for look-up table and plots
# bin parameters for q in units of k = Evald's sphere radius [1/A]
bpq = BinPars((-0.25, 0.25), 1000, vtype=np.float32, endpoint=False)
# bin parameters for omega [degree] - fiber rotation angle around axis
bpomega = BinPars((0., 180.), 360, vtype=np.float32, endpoint=False)
# bin parameters for beta [degree] - fiber axis tilt angle
#bpbeta = BinPars((15., 195.), 2, vtype=np.float32, endpoint=True)
#bpbeta = BinPars((15., 15.), 1, vtype=np.float32, endpoint=False)
#bpbeta = BinPars((5., 25.), 2, vtype=np.float32, endpoint=True)
bpbeta = BinPars((0., 50.), 11, vtype=np.float32, endpoint=True)
bpbeta2 = BinPars((180., 230.), 11, vtype=np.float32, endpoint=True)
str_beta = 'for-beta:%s' % (bpbeta.strrange)
print '\n%s\nIndexing lookup table\n' % (91 * '_')
lut = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32,
evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega,
bpbeta)
lut2 = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32,
evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega,
bpbeta2)
fout.close()
print '\nIndexing lookup table is saved in the file: %s' % fname
#------------------------------
# produce and save plots
import algos.graph.GlobalGraphics as gg
img = lut # or lut2
img = lut + lut2
img_range = (bpq.vmin, bpq.vmax, bpomega.vmax, bpomega.vmin)
axim = gg.plotImageLarge(lut, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Non-symmetrized for beta', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Symmetrized for beta (beta, beta+pi)', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-sym-%s.png' % (prefix, str_beta),
pbits=1)
arrhi = np.sum(img, 0)
fighi, axhi, hi = gg.hist1d(bpq.binedges, bins=bpq.nbins-1, amp_range=(bpq.vmin, bpq.vmax), weights=arrhi,\
color='b', show_stat=True, log=False,\
figsize=(15,5), axwin=(0.05, 0.12, 0.85, 0.80),\
title=None, xlabel='$q_{H}$ ($1/\AA$)', ylabel='Intensity', titwin=None)
gg.show()
gg.save_fig(fighi,
'%splot-his-prob-vs-qh-%s.png' % (prefix, str_beta),
pbits=1)
qh_weight = zip(bpq.bincenters, arrhi)
fname = '%sarr-qh-weight-%s.npy' % (prefix, str_beta)
print 'Save qh:weigt array in file %s' % fname
np.save(fname, qh_weight)
def plot_lattice(b1 = (1.,0.,0.), b2 = (0.,1.,0.), b3 = (0.,0.,1.),\
hmax=3, kmax=2, lmax=1, cdtype=np.float32,\
evald_rad=0.5, qtol=0.01, prefix='', do_movie=False, delay=400) :
"""Plots 2-d reciprocal space lattice, evald sphere,
generates series of plots for rotated lattice and movie from these plots.
- do_movie = True/False - on/off production of movie
- delay - is a time in msec between movie frames.
"""
import matplotlib.pyplot as plt
import algos.graph.GlobalGraphics as gg
print '\nIn %s' % sys._getframe().f_code.co_name
print '%s\nTest lattice with default parameters' % (80*'_')
x, y, z, r, h, k, l = lattice(b1, b2, b3, hmax, kmax, lmax, cdtype)
xlimits = ylimits = (-0.3, 0.3) # plot limits in (1/A)
#ylimits = (-0.4, 0.4) # plot limits in (1/A)
#xlimits = (-0.5, 0.3) # plot limits in (1/A)
fig, ax = gg.plotGraph(x,y, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.86), pfmt='bo')
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.save_fig(fig, '%sreciprocal-space-lattice.png' % prefix, pbits=1)
lst_omega = range(0,180,2) if do_movie else range(0,13,11)
#lst_omega = range(0,180,5) if do_movie else range(0,13,11)
#lst_omega = range(0,180,45) if do_movie else range(0,13,11)
beta_deg = 0
for omega_deg in lst_omega :
xrot1, yrot1 = rotation(x, y, omega_deg)
xrot2, zrot2 = rotation(xrot1, z, beta_deg)
dr, qv, qh = radial_distance(xrot2, yrot1, zrot2, evald_rad)
xhit = [xr for dq,xr in zip(dr.flatten(), xrot2.flatten()) if math.fabs(dq)<qtol]
yhit = [yr for dq,yr in zip(dr.flatten(), yrot1.flatten()) if math.fabs(dq)<qtol]
#fig, ax = gg.plotGraph(xrot2, yrot1, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.84), pfmt='bo')
ax.cla()
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.plot(xrot1, yrot1, 'yo')
if len(xhit)>0 and len(yhit)>0 : ax.plot(xhit, yhit, 'bo')
ax.set_title('beta=%.0f omega=%.0f' % (beta_deg, omega_deg), color='k', fontsize=20)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.drawCenter(ax, (-evald_rad,0), s=0.04, linewidth=2, color='k')
gg.drawCircle(ax, (-evald_rad,0), evald_rad, linewidth=1, color='k', fill=False)
fig.canvas.draw()
gg.show('Do not hold!')
gg.save_fig(fig, '%sreciprocal-space-lattice-rotated-beta=%03d-omega=%03d.png'%\
(prefix, int(beta_deg), int(omega_deg)), pbits=1)
if do_movie :
import os
#dir_movie = 'movie'
#os.system('mkdir %s'% dir_movie)
cmd = 'convert -delay %f %sreciprocal-space-lattice-rotated-beta=*.png movie.gif' % (delay, prefix)
print 'Wait for completion of the command: %s' % cmd
os.system(cmd)
print 'DONE!'
gg.show()
def plot_lattice(b1 = (1.,0.,0.), b2 = (0.,1.,0.), b3 = (0.,0.,1.),\
hmax=3, kmax=2, lmax=1, cdtype=np.float32,\
evald_rad=0.5, qtol=0.01, prefix='', do_movie=False, delay=400) :
"""Plots 2-d reciprocal space lattice, evald sphere,
generates series of plots for rotated lattice and movie from these plots.
- do_movie = True/False - on/off production of movie
- delay - is a time in msec between movie frames.
"""
import matplotlib.pyplot as plt
import algos.graph.GlobalGraphics as gg
print '\nIn %s' % sys._getframe().f_code.co_name
print '%s\nTest lattice with default parameters' % (80 * '_')
x, y, z, r, h, k, l = lattice(b1, b2, b3, hmax, kmax, lmax, cdtype)
xlimits = ylimits = (-0.3, 0.3) # plot limits in (1/A)
#ylimits = (-0.4, 0.4) # plot limits in (1/A)
#xlimits = (-0.5, 0.3) # plot limits in (1/A)
fig, ax = gg.plotGraph(x,
y,
figsize=(8, 7.5),
window=(0.15, 0.10, 0.78, 0.86),
pfmt='bo')
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.save_fig(fig, '%sreciprocal-space-lattice.png' % prefix, pbits=1)
lst_omega = range(0, 180, 2) if do_movie else range(0, 13, 11)
#lst_omega = range(0,180,5) if do_movie else range(0,13,11)
#lst_omega = range(0,180,45) if do_movie else range(0,13,11)
beta_deg = 0
for omega_deg in lst_omega:
xrot1, yrot1 = rotation(x, y, omega_deg)
xrot2, zrot2 = rotation(xrot1, z, beta_deg)
dr, qv, qh = radial_distance(xrot2, yrot1, zrot2, evald_rad)
xhit = [
xr for dq, xr in zip(dr.flatten(), xrot2.flatten())
if math.fabs(dq) < qtol
]
yhit = [
yr for dq, yr in zip(dr.flatten(), yrot1.flatten())
if math.fabs(dq) < qtol
]
#fig, ax = gg.plotGraph(xrot2, yrot1, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.84), pfmt='bo')
ax.cla()
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.plot(xrot1, yrot1, 'yo')
if len(xhit) > 0 and len(yhit) > 0: ax.plot(xhit, yhit, 'bo')
ax.set_title('beta=%.0f omega=%.0f' % (beta_deg, omega_deg),
color='k',
fontsize=20)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.drawCenter(ax, (-evald_rad, 0), s=0.04, linewidth=2, color='k')
gg.drawCircle(ax, (-evald_rad, 0),
evald_rad,
linewidth=1,
color='k',
fill=False)
fig.canvas.draw()
gg.show('Do not hold!')
gg.save_fig(fig, '%sreciprocal-space-lattice-rotated-beta=%03d-omega=%03d.png'%\
(prefix, int(beta_deg), int(omega_deg)), pbits=1)
if do_movie:
import os
#dir_movie = 'movie'
#os.system('mkdir %s'% dir_movie)
cmd = 'convert -delay %f %sreciprocal-space-lattice-rotated-beta=*.png movie.gif' % (
delay, prefix)
print 'Wait for completion of the command: %s' % cmd
os.system(cmd)
print 'DONE!'
gg.show()