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# -*- coding: utf-8 -*-
u"""
Reflection from mosaic crystal
"""
__author__ = "Konstantin Klementiev"
__date__ = "2018/08/03"
import sys
import os
import numpy as np
import pickle
import os, sys; sys.path.append(os.path.join('..', '..')) # analysis:ignore
import xrt.backends.raycing.sources as rsources
import xrt.backends.raycing.screens as rscreens
import xrt.backends.raycing.materials as rmats
import xrt.backends.raycing.oes as roes
import xrt.backends.raycing.run as rrun
import xrt.backends.raycing as raycing
import xrt.plotter as xrtplot
import xrt.runner as xrtrun
hkl = (0, 0, 2)
#hkl = (0, 0, 6)
shlk = ''.join(['{0}'.format(i) for i in hkl])
kw = dict(hkl=hkl, a=2.456, c=6.696, gamma=120,
atoms=[6]*4, atomsXYZ=[[0., 0., 0.], [0., 0., 0.5],
[1./3, 2./3, 0.], [2./3, 1./3, 0.5]],
table='Chantler')
xtalPerfect = rmats.CrystalFromCell('perfect', **kw)
mosaicityFWHMdeg = 0.4 # = 0.4° fwhm
mosaicityFWHM = np.deg2rad(mosaicityFWHMdeg)
mosaicity = mosaicityFWHM/2.355
xtalMosaic = rmats.CrystalFromCell('mosaic', **kw, mosaicity=mosaicity)
#Ec = 3000.
Ec = 8000.
#Ec = 17000.
dE = 2e-4*Ec
nrays = 1e6
p = 1e4
#screenPoss = np.array([1.5, 2, 2.5, 3]) * p
screenPoss = np.array([2, 3]) * p
xBins = 160
zBins = 100
def build_beamline():
beamLine = raycing.BeamLine()
bragg = xtalPerfect.get_Bragg_angle(Ec) - xtalPerfect.get_dtheta(Ec)
print('theta={0}deg'.format(np.degrees(bragg)))
print('dtheta', xtalPerfect.get_dtheta(Ec), 'mosaicity', mosaicityFWHM/2.355)
beamLine.bragg = bragg
print("mosaic divergence hor", 2*mosaicityFWHM*np.sin(bragg))
beamLine.source = rsources.GeometricSource(
beamLine, center=[0, 0, 0],
distx=None, disty=None, distz=None,
# for reflectivity calculations select larger dzprime:
# distxprime=None, distzprime='flat', dzprime=0.022,
# distE='lines', energies=[Ec], polarization='h',
# for getting diffracted images select this one:
distxprime='flat', distzprime='flat', dxprime=1e-3, dzprime=2e-4,
distE='flat', energies=(Ec-dE/2, Ec+dE/2), polarization='h',
nrays=nrays,
pitch=-bragg)
beamLine.hX = p * np.tan(bragg)
kwOE = dict(bl=beamLine, center=[0, p, -beamLine.hX], limPhysY=[-1e4, 1e4])
# beamLine.xtalP = roes.OE(**kwOE, material=xtalPerfect)
beamLine.xtalM = roes.OE(**kwOE, material=xtalMosaic)
beamLine.screen = rscreens.Screen(beamLine, center=[0, 2*p, 0])
return beamLine
def run_process(beamLine):
beamSource = beamLine.source.shine()
# beamXtalGlobal, beamXtalLocal = beamLine.xtalP.reflect(beamSource)
beamXtalGlobal, beamXtalLocal = beamLine.xtalM.reflect(beamSource)
raycing.rotate_beam(beamSource, pitch=beamLine.bragg)
beamSource.dtheta = beamSource.c/beamSource.b
beamXtalLocal.dtheta = beamSource.dtheta
outD = {'beamSource': beamSource,
'beamXtalGlobal': beamXtalGlobal, 'beamXtalLocal': beamXtalLocal}
for iscr, screenPos in enumerate(screenPoss):
hs = beamLine.hX * (-1 + (screenPos-p)/p)
beamLine.screen.center = [0, screenPos, hs]
beamScreen = beamLine.screen.expose(beamXtalGlobal)
outD['beamScreen'+'{0:d}'.format(iscr)] = beamScreen
return outD
rrun.run_process = run_process
def get_dtheta(beam):
return beam.dtheta
def define_plots(beamLine):
plots = []
plot = xrtplot.XYCPlot(
beam=r"beamSource", aspect='auto',
xaxis=xrtplot.XYCAxis(r"x'", 'mrad'),
yaxis=xrtplot.XYCAxis(r"z'", 'mrad', data=get_dtheta))
plot.saveName = ["0-source.png"]
plots.append(plot)
plot = xrtplot.XYCPlot(
beam=r"beamXtalLocal", aspect='auto',
xaxis=xrtplot.XYCAxis(r"x'", 'mrad'),
yaxis=xrtplot.XYCAxis(r"z'", 'mrad', data=get_dtheta))
plot.saveName = ["1-localXtal.png"]
plots.append(plot)
plot = xrtplot.XYCPlot(
beam=r"beamXtalLocal", aspect='auto',
xaxis=xrtplot.XYCAxis(r"y", 'mm'),
yaxis=xrtplot.XYCAxis(r"z", 'µm', limits=[-400, 10]))
plot.saveName = ["1-localXtalDepth.png"]
plots.append(plot)
for iscr, screenPos in enumerate(screenPoss):
plot = xrtplot.XYCPlot(
beam='beamScreen'+'{0:d}'.format(iscr), aspect='auto',
xaxis=xrtplot.XYCAxis(r"x", limits=[-100, 100], bins=xBins),
yaxis=xrtplot.XYCAxis(r"z", limits=[-3.6, 3.6], bins=zBins))
plot.textPanel = plot.fig.text(
0.88, 0.9, 'p:q = 1:{0:.0f}'.format((screenPos-p)/p),
transform=plot.fig.transFigure, size=14, color='r',
ha='center')
plot.saveName = ["2-screen{0:d}.png".format(iscr+1)]
plots.append(plot)
for plot in plots:
plot.caxis.offset = Ec
plot.xaxis.fwhmFormatStr = '%.2f'
plot.yaxis.fwhmFormatStr = '%.2f'
return plots
def afterScript(plots, beamLine):
sax = plots[0].yaxis
rax = plots[1].yaxis
dax = plots[2].yaxis
fn = 'reflMosaicGraphite{0}-{1:02.0f}keV-{2}deg.pickle'.format(
shlk, Ec*1e-3, mosaicityFWHMdeg)
with open(fn, 'wb') as f:
pickle.dump([sax.binCenters, sax.total1D, rax.total1D,
dax.binCenters, dax.total1D, plots[0].nRaysGood], f)
print("Saved")
def calc_refl(E):
delta = np.linspace(-0.011, 0.011, 221)
thetaB = xtalMosaic.get_Bragg_angle(E) - xtalMosaic.get_dtheta(E)
beamInDotNormal = -np.sin(thetaB + delta)
rs, rp = xtalMosaic.get_amplitude_mosaic(E, beamInDotNormal)
return delta, rs, rp
def plot_reflectivity(fromRayTracing=False):
import matplotlib.pyplot as plt
from matplotlib.legend_handler import HandlerBase
class NLineObjectsHandler(HandlerBase):
def create_artists(self, legend, orig_handles,
x0, y0, width, height, fontsize, trans):
return [plt.Line2D([x0, x0+width], [p*height, p*height],
linestyle=handle.get_linestyle(),
color=handle.get_color()) for handle, p in
zip(orig_handles, self.get_line_vpos(len(orig_handles)))]
def get_line_vpos(self, n):
if n == 1:
pos = [0.5]
elif n == 2:
pos = [0.7, 0.3]
elif n == 3:
pos = [0.9, 0.5, 0.1]
elif n == 4:
pos = [0.95, 0.65, 0.35, 0.05]
else:
raise ValueError('too many lines')
return pos
ms = "{0}°".format(mosaicityFWHMdeg)
fig = plt.figure(1)
fig.suptitle("\nRocking curves for graphite "
"({0}) with mosaicity FWHM ".format(shlk)+ms, fontsize=12)
ax = fig.add_subplot(111)
ax.set_xlabel(r'$\theta-\theta_B$ (mrad)')
ax.set_ylabel('reflectivity s')
if fromRayTracing:
fig2 = plt.figure(2)
fig2.suptitle("\nDepth distribution for graphite "
"({0}) with mosaicity FWHM ".format(shlk)+ms,
fontsize=12)
ax2 = fig2.add_subplot(111)
ax2.set_xlabel(r'z (µm)')
ax2.set_ylabel('relative weight (a.u.)')
lxrt, lxc, labels = [], [], []
for E0, color in zip([3, 8, 17], ['C0', 'C1', 'C2']):
if fromRayTracing:
fn = 'reflMosaicGraphite{0}-{1:02.0f}keV-{2}deg.pickle'.format(
shlk, E0, mosaicityFWHMdeg)
with open(fn, 'rb') as f:
delta, source, refl, z, nz, raysGood = pickle.load(f)
source[source == 0] = 1.
refl /= source
else:
delta, rs, rp = calc_refl(E0*1e3)
delta *= 1e3
refl = rs**2
label = '{0:.0f} keV'.format(E0)
labels.append(label)
l, = ax.plot(delta, refl, '--', color=color, lw=1.5)
lxrt.append(l)
fnx = 'graphite{0}_mosaic{1:02.0f}_{2:02.0f}kev.xc.gz'.format(
shlk, mosaicityFWHMdeg*10, E0)
path = os.path.join('', 'XOP-RockingCurves', fnx)
x, reflXOP = np.loadtxt(path, unpack=True)
l, = ax.plot(x*1e3, reflXOP, '-', color=color, lw=1.5)
lxc.append(l)
if fromRayTracing:
ax2.plot(-z, nz/nz.sum(), '-', color=color, lw=1.5, label=label)
ax.set_xlim([delta.min(), delta.max()])
ax.set_ylim([0, None])
leg1 = ax.legend([(l1, l2) for l1, l2 in zip(lxrt, lxc)], labels,
handler_map={tuple: NLineObjectsHandler()},
loc='upper right')
leg2 = ax.legend([tuple(lxrt), tuple(lxc)],
[r'xrt', r'XCrystal/XOP'],
handler_map={tuple: NLineObjectsHandler()},
loc='upper left')
ax.add_artist(leg1)
ax.add_artist(leg2)
if fromRayTracing:
ax2.set_xlim([0, abs(z).max()])
ax2.set_ylim([0, None])
ax2.legend(loc='upper right')
fname = 'MosaicGraphite{0}-ReflectivityS'.format(shlk)
fig.savefig(fname + '.png')
if fromRayTracing:
fname2 = 'MosaicGraphite{0}-Z'.format(shlk)
fig2.savefig(fname2 + '.png')
plt.show()
def main():
beamLine = build_beamline()
plots = define_plots(beamLine)
xrtrun.run_ray_tracing(plots=plots, repeats=1, beamLine=beamLine,
afterScript=afterScript,
afterScriptArgs=[plots, beamLine])
if __name__ == '__main__':
# main()
plot_reflectivity()
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