# -*- coding: utf-8 -*-
"""
Tests for Materials
-------------------

The module compares reflectivity, transmittivity, refraction index,
absorption coefficient etc. with those calculated by XOP.

Various material properties are compared with those calculated by XCrystal/XOP
(also used by shadow for modeling crystal optics), XInpro/XOP and others.

Find the corresponding scripts in `tests/raycing` directory.

Reflectivity of Bragg crystals
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The small amplitude differences with XOP results are due
to slight differences in Debye-Waller factor and/or tabulated values of the
atomic scattering factors. The phase difference between s- and p-polarized
rays (calculated by xrt, cyan line, right Y axis) is not calculated by the
XOP programs and therefore is given without comparison.

+-------+--------------------+------------------+-------------------+
|       |      α = -5°       |    symmetric     |       α = 5°      |
+=======+====================+==================+===================+
| thick | |bSi111_thick_-5|  | |bSi111_thick_0| | |bSi111_thick_5|  |
|       | |bSi333_thick_-5|  | |bSi333_thick_0| | |bSi333_thick_5|  |
+-------+--------------------+------------------+-------------------+
| 100 µm|   |bSi111_100_-5|  |  |bSi111_100_0|  |  |bSi111_100_5|   |
|       |   |bSi333_100_-5|  |  |bSi333_100_0|  |  |bSi333_100_5|   |
+-------+--------------------+------------------+-------------------+
| 7 µm  |   |bSi111_007_-5|  |  |bSi111_007_0|  |  |bSi111_007_5|   |
|       |   |bSi333_007_-5|  |  |bSi333_007_0|  |  |bSi333_007_5|   |
+-------+--------------------+------------------+-------------------+

.. |bSi111_thick_-5| imagezoom:: _images/bSi111_thick_-5.*
.. |bSi111_thick_0| imagezoom:: _images/bSi111_thick_0.*
.. |bSi111_thick_5| imagezoom:: _images/bSi111_thick_5.*
   :loc: upper-right-corner
.. |bSi111_100_-5| imagezoom:: _images/bSi111_100mum_-5.*
.. |bSi111_100_0| imagezoom:: _images/bSi111_100mum_0.*
.. |bSi111_100_5| imagezoom:: _images/bSi111_100mum_5.*
   :loc: upper-right-corner
.. |bSi111_007_-5| imagezoom:: _images/bSi111_007mum_-5.*
.. |bSi111_007_0| imagezoom:: _images/bSi111_007mum_0.*
.. |bSi111_007_5| imagezoom:: _images/bSi111_007mum_5.*
   :loc: upper-right-corner

.. |bSi333_thick_-5| imagezoom:: _images/bSi333_thick_-5.*
.. |bSi333_thick_0| imagezoom:: _images/bSi333_thick_0.*
.. |bSi333_thick_5| imagezoom:: _images/bSi333_thick_5.*
   :loc: upper-right-corner
.. |bSi333_100_-5| imagezoom:: _images/bSi333_100mum_-5.*
.. |bSi333_100_0| imagezoom:: _images/bSi333_100mum_0.*
.. |bSi333_100_5| imagezoom:: _images/bSi333_100mum_5.*
   :loc: upper-right-corner
.. |bSi333_007_-5| imagezoom:: _images/bSi333_007mum_-5.*
.. |bSi333_007_0| imagezoom:: _images/bSi333_007mum_0.*
.. |bSi333_007_5| imagezoom:: _images/bSi333_007mum_5.*
   :loc: upper-right-corner

Reflectivity of Laue crystals
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The small amplitude differences with XOP results are due
to slight differences in Debye-Waller factor and/or tabulated values of the
atomic scattering factors. The phase difference between s- and p-polarized
rays (calculated by xrt, cyan line, right Y axis) is not calculated by the
XOP programs and therefore is given without comparison.

+-------+--------------------+------------------+-------------------+
|       |      α = -5°       |    symmetric     |       α = 5°      |
+=======+====================+==================+===================+
| 100 µm|   |lSi111_100_-5|  |  |lSi111_100_0|  |  |lSi111_100_5|   |
|       |   |lSi333_100_-5|  |  |lSi333_100_0|  |  |lSi333_100_5|   |
+-------+--------------------+------------------+-------------------+
| 7 µm  |   |lSi111_007_-5|  |  |lSi111_007_0|  |  |lSi111_007_5|   |
|       |   |lSi333_007_-5|  |  |lSi333_007_0|  |  |lSi333_007_5|   |
+-------+--------------------+------------------+-------------------+

.. |lSi111_100_-5| imagezoom:: _images/lSi111_100mum_-5.*
.. |lSi111_100_0| imagezoom:: _images/lSi111_100mum_0.*
.. |lSi111_100_5| imagezoom:: _images/lSi111_100mum_5.*
   :loc: upper-right-corner
.. |lSi111_007_-5| imagezoom:: _images/lSi111_007mum_-5.*
.. |lSi111_007_0| imagezoom:: _images/lSi111_007mum_0.*
.. |lSi111_007_5| imagezoom:: _images/lSi111_007mum_5.*
   :loc: upper-right-corner

.. |lSi333_100_-5| imagezoom:: _images/lSi333_100mum_-5.*
.. |lSi333_100_0| imagezoom:: _images/lSi333_100mum_0.*
.. |lSi333_100_5| imagezoom:: _images/lSi333_100mum_5.*
   :loc: upper-right-corner
.. |lSi333_007_-5| imagezoom:: _images/lSi333_007mum_-5.*
.. |lSi333_007_0| imagezoom:: _images/lSi333_007mum_0.*
.. |lSi333_007_5| imagezoom:: _images/lSi333_007mum_5.*
   :loc: upper-right-corner

.. _transmittivity_Bragg:

Transmittivity of Bragg crystals
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The curves are basically equal only for the symmetric case. Both
XCrystal/XOP and XInpro/XOP are different for asymmetric crystals, when they
give too low or too high (>1) transmittivity. This is because they refer to
intencities, not flux and therefore cannot be directly applied to rays in
ray tracing.

+-------+--------------------+-------------------+--------------------+
|       |      α = -5°       |     symmetric     |        α = 5°      |
+=======+====================+===================+====================+
| 100 µm|  |btSi111_100_-5|  |  |btSi111_100_0|  |  |btSi111_100_5|   |
|       |  |btSi333_100_-5|  |  |btSi333_100_0|  |  |btSi333_100_5|   |
+-------+--------------------+-------------------+--------------------+
| 7 µm  |  |btSi111_007_-5|  |  |btSi111_007_0|  |  |btSi111_007_5|   |
|       |  |btSi333_007_-5|  |  |btSi333_007_0|  |  |btSi333_007_5|   |
+-------+--------------------+-------------------+--------------------+

.. |btSi111_100_-5| imagezoom:: _images/btSi111_100mum_-5.*
.. |btSi111_100_0| imagezoom:: _images/btSi111_100mum_0.*
.. |btSi111_100_5| imagezoom:: _images/btSi111_100mum_5.*
   :loc: upper-right-corner
.. |btSi111_007_-5| imagezoom:: _images/btSi111_007mum_-5.*
.. |btSi111_007_0| imagezoom:: _images/btSi111_007mum_0.*
.. |btSi111_007_5| imagezoom:: _images/btSi111_007mum_5.*
   :loc: upper-right-corner

.. |btSi333_100_-5| imagezoom:: _images/btSi333_100mum_-5.*
.. |btSi333_100_0| imagezoom:: _images/btSi333_100mum_0.*
.. |btSi333_100_5| imagezoom:: _images/btSi333_100mum_5.*
   :loc: upper-right-corner
.. |btSi333_007_-5| imagezoom:: _images/btSi333_007mum_-5.*
.. |btSi333_007_0| imagezoom:: _images/btSi333_007mum_0.*
.. |btSi333_007_5| imagezoom:: _images/btSi333_007mum_5.*
   :loc: upper-right-corner

Transmittivity of Laue crystals
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The curves are basically equal only for the symmetric case and only with
XInpro/XOP results. XInpro/XOP is wrong for asymmetric crystals, when it
gives too low or too high (>1) transmittivity. As seen, XCrystal/XOP is
essentially different and wrong with Laue transmittivity.

+-------+--------------------+-------------------+--------------------+
|       |      α = -5°       |    symmetric      |        α = 5°      |
+=======+====================+===================+====================+
| 100 µm|  |ltSi111_100_-5|  |  |ltSi111_100_0|  |  |ltSi111_100_5|   |
|       |  |ltSi333_100_-5|  |  |ltSi333_100_0|  |  |ltSi333_100_5|   |
+-------+--------------------+-------------------+--------------------+
| 7 µm  |  |ltSi111_007_-5|  |  |ltSi111_007_0|  |  |ltSi111_007_5|   |
|       |  |ltSi333_007_-5|  |  |ltSi333_007_0|  |  |ltSi333_007_5|   |
+-------+--------------------+-------------------+--------------------+

.. |ltSi111_100_-5| imagezoom:: _images/ltSi111_100mum_-5.*
.. |ltSi111_100_0| imagezoom:: _images/ltSi111_100mum_0.*
.. |ltSi111_100_5| imagezoom:: _images/ltSi111_100mum_5.*
   :loc: upper-right-corner
.. |ltSi111_007_-5| imagezoom:: _images/ltSi111_007mum_-5.*
.. |ltSi111_007_0| imagezoom:: _images/ltSi111_007mum_0.*
.. |ltSi111_007_5| imagezoom:: _images/ltSi111_007mum_5.*
   :loc: upper-right-corner

.. |ltSi333_100_-5| imagezoom:: _images/ltSi333_100mum_-5.*
.. |ltSi333_100_0| imagezoom:: _images/ltSi333_100mum_0.*
.. |ltSi333_100_5| imagezoom:: _images/ltSi333_100mum_5.*
   :loc: upper-right-corner
.. |ltSi333_007_-5| imagezoom:: _images/ltSi333_007mum_-5.*
.. |ltSi333_007_0| imagezoom:: _images/ltSi333_007mum_0.*
.. |ltSi333_007_5| imagezoom:: _images/ltSi333_007mum_5.*
   :loc: upper-right-corner

.. _tests_mosaic:

Reflectivity of mosaic crystals
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

These tests implement the diffraction setup from [SanchezDelRioMosaic]_, Fig.
4. In our case, the source has a finite energy band to demonstrate the energy
dispersion effect in parafocusing (cf. Figs. 5 and 6 ibid).

.. imagezoom:: _images/MosaicGraphite002-screenA.*
.. imagezoom:: _images/MosaicGraphite002-screenB.*

The penetration depth distribution should be compared with Fig 7 ibid.

.. imagezoom:: _images/MosaicGraphite002-Z.*

The reflectivity curves are compared with those by XCrystal/XOP [XOP]_. The
small differences are primarily due to small differences in the tabulations of
the scattering factors. We use the one by Chantler [Chantler]_.

.. imagezoom:: _images/MosaicGraphite002-ReflectivityS.*

Mirror reflectivity
~~~~~~~~~~~~~~~~~~~

The small amplitude differences with XOP are due
to slight differences in tabulated values of the atomic scattering factors.
The phase difference between s- and p-polarized rays (calculated by xrt,
cyan line, right Y axis) is not calculated by the XOP programs and
therefore is given without comparison.

.. imagezoom:: _images/MirrorReflSi@0.5deg.*
.. imagezoom:: _images/MirrorReflSiO2@0.5deg.*
   :loc: upper-right-corner

.. imagezoom:: _images/MirrorReflRh@2mrad.*
.. imagezoom:: _images/MirrorReflPt@4mrad.*
   :loc: upper-right-corner

.. _multilayer_reflectivity:

Slab, multilayer and coating reflectivity
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The phase difference between s- and p-polarized rays is given without
comparison.

.. imagezoom:: _images/SlabReflW.*
.. imagezoom:: _images/MultilayerSiW.*
   :loc: upper-right-corner

.. imagezoom:: _images/MultilayerSiW-graded.*
.. imagezoom:: _images/MultilayerSiWCXRO_id0.*
   :loc: upper-right-corner

.. imagezoom:: _images/MultilayerSiWCXRO_id6.*
.. imagezoom:: _images/MirrorRefl30nmRhOnSi_4mrad_RMSroughness2nm.*
   :loc: upper-right-corner

.. imagezoom:: _images/MirrorRefl20nmDiamondOnQuartz_0.2deg_RMSroughness1nm.*

Transmittivity of materials
~~~~~~~~~~~~~~~~~~~~~~~~~~~

The small amplitude differences with XOP are due
to slight differences in tabulated values of the atomic scattering factors.

.. imagezoom:: _images/TransmDiamond.*

Absorption of materials
~~~~~~~~~~~~~~~~~~~~~~~

The deviations at low energies due to differences in tabulated values of the
atomic scattering factors.

.. imagezoom:: _images/AbsorptionBe.*
.. imagezoom:: _images/AbsorptionNi.*
   :loc: upper-right-corner

.. imagezoom:: _images/AbsorptionAu.*

"""
__author__ = "Konstantin Klementiev"
__date__ = "12 Mar 2014"

import math
#import cmath
import numpy as np
import matplotlib as mpl
mpl.rcParams['backend'] = 'Qt5Agg'
import matplotlib.pyplot as plt

import os, sys; sys.path.append(os.path.join('..', '..'))  # analysis:ignore
import xrt.backends.raycing.materials as rm


def compare_rocking_curves(hkl, t=None, geom='Bragg reflected', factDW=1.,
                           legendPos1=4, legendPos2=1):
    """A comparison subroutine used in the module test suit."""
    def for_one_alpha(crystal, alphaDeg, hkl):
        alpha = math.radians(alphaDeg)
        s0 = (np.zeros_like(theta), np.cos(theta+alpha), -np.sin(theta+alpha))
        sh = (np.zeros_like(theta), np.cos(theta-alpha), np.sin(theta-alpha))
        if geom.startswith('Bragg'):
            n = (0, 0, 1)  # outward surface normal
        else:
            n = (0, -1, 0)  # outward surface normal
        hn = (0, math.sin(alpha), math.cos(alpha))  # outward Bragg normal
        gamma0 = sum(i*j for i, j in zip(n, s0))
        gammah = sum(i*j for i, j in zip(n, sh))
        hns0 = sum(i*j for i, j in zip(hn, s0))

        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.88)
        ax = fig.add_subplot(111)

#        curS, curP = crystal.get_amplitude_Authie(E, gamma0, gammah, hns0)
#        p5, = ax.plot((theta - thetaCenter) * convFactor, abs(curS)**2, '-g')
#        p6, = ax.plot((theta - thetaCenter) * convFactor, abs(curP)**2, '--g')
        curS, curP = crystal.get_amplitude(E, gamma0, gammah, hns0)
# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(curS * curP.conj()))
        p9, = ax2.plot((theta-thetaCenter) * convFactor, phi, 'c', lw=1,
                       yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')

        if t is not None:
            tt = u', t={0:.0f}µm'.format(t * 1e3)
            tname = '{0:03d}mum'.format(int(t * 1e3))
        else:
            tt = ' thick'
            tname = 'thick'
        if geom.startswith('Bragg'):
            geomPrefix = 'b'
        else:
            geomPrefix = 'l'
        if geom.endswith('transmitted'):
            geomPrefix += 't'
        fig.suptitle(r'{0} Si{1}, $\alpha={2:.1f}^\circ${3}'.format(geom,
                     hkl, alphaDeg, tt), fontsize=16)

        path = os.path.join('', 'XOP-RockingCurves') + os.sep
        x, R2s = np.loadtxt("{0}{1}Si{2}_{3}_{4:-.0f}_s.xc.gz".format(path,
                            geomPrefix, hkl, tname, alphaDeg), unpack=True)
        p1, = ax.plot(x, R2s, '-k', label='s XCrystal')
        x, R2p = np.loadtxt("{0}{1}Si{2}_{3}_{4:-.0f}_p.xc.gz".format(path,
                            geomPrefix, hkl, tname, alphaDeg), unpack=True)
        p2, = ax.plot(x, R2p, '--k', label='p XCrystal')

        x, R2s = np.loadtxt("{0}{1}Si{2}_{3}_{4:-.0f}_s.xin.gz".format(path,
                            geomPrefix, hkl, tname, alphaDeg), unpack=True)
        p3, = ax.plot(x, R2s, '-b', label='s XInpro')
        x, R2p = np.loadtxt("{0}{1}Si{2}_{3}_{4:-.0f}_p.xin.gz".format(path,
                            geomPrefix, hkl, tname, alphaDeg), unpack=True)
        p4, = ax.plot(x, R2p, '--b', label='p XInpro')

        p7, = ax.plot((theta - thetaCenter) * convFactor, abs(curS)**2, '-r')
        p8, = ax.plot((theta - thetaCenter) * convFactor, abs(curP)**2, '--r')
        ax.set_xlabel(r'$\theta-\theta_B$ (arcsec)')
        if geom.endswith('transmitted'):
            ax.set_ylabel('transmittivity')
        else:
            ax.set_ylabel('reflectivity')
        ax.set_xlim([dtheta[0] * convFactor, dtheta[-1] * convFactor])
#upper right	1
#upper left	2
#lower left	3
#lower right	4
#right   	5
#center left	6
#center right	7
#lower center	8
#upper center	9
#center         10
        l1 = ax2.legend([p1, p2], ['s', 'p'], loc=legendPos1)
#        ax.legend([p1, p3, p5, p7], ['XCrystal/XOP', 'XInpro/XOP',
#        'pxrt-Authier', 'pxrt-Bel&Dm'], loc=1)
        ax2.legend([p1, p3, p7], ['XCrystal/XOP', 'XInpro/XOP', 'xrt'],
                   loc=legendPos2)
        ax2.add_artist(l1)

        fname = '{0}Si{1}_{2}_{3:-.0f}'.format(
            geomPrefix, hkl, tname, alphaDeg)
        fig.savefig(fname + '.png')

    E0 = 10000.
    convFactor = 180 / math.pi * 3600.  # arcsec
    if hkl == '111':  # Si111
        if geom.startswith('Bragg'):
            dtheta = np.linspace(0, 100, 400) * 1e-6
        else:
            dtheta = np.linspace(-50, 50, 400) * 1e-6
        dSpacing = 3.13562
        hklInd = 1, 1, 1
    elif hkl == '333':  # Si333
        if geom.startswith('Bragg'):
            dtheta = np.linspace(0, 30, 400) * 1e-6
        else:
            dtheta = np.linspace(-15, 15, 400) * 1e-6
        dSpacing = 3.13562 / 3
        hklInd = 3, 3, 3

    siCrystal = rm.CrystalDiamond(hklInd, dSpacing, t=t, geom=geom,
                                  factDW=factDW)
    thetaCenter = math.asin(rm.ch / (2*siCrystal.d*E0))

    E = np.ones_like(dtheta) * E0
    theta = dtheta + thetaCenter
    for_one_alpha(siCrystal, 0., hkl)
    for_one_alpha(siCrystal, -5., hkl)
    for_one_alpha(siCrystal, 5., hkl)


def compare_rocking_curves_bent(hkl, t=None, geom='Laue reflected', factDW=1.,
                                legendPos1=4, legendPos2=1, Rcurvmm=None,
                                alphas=[0]):
    try:
        import pyopencl as cl
        os.environ['PYOPENCL_COMPILER_OUTPUT'] = '1'
        isOpenCL = True
    except ImportError:
        isOpenCL = False

    if isOpenCL:
        import xrt.backends.raycing.myopencl as mcl
        matCL = mcl.XRT_CL(r'materials.cl',
                           # targetOpenCL='CPU'
                           )
    else:
        matCL = None

    """A comparison subroutine used in the module test suit."""
    def for_one_alpha(crystal, alphaDeg, hkl):
        xcb_tt = True
        xcb_pp = False

        Rcurv=np.inf if Rcurvmm is None else Rcurvmm
        if Rcurv==0:
            Rcurv=np.inf
        alpha = np.radians(alphaDeg)
        s0 = (np.zeros_like(theta), np.cos(theta+alpha), -np.sin(theta+alpha))
        sh = (np.zeros_like(theta), np.cos(theta-alpha), np.sin(theta-alpha))
        if geom.startswith('Bragg'):
            n = (0, 0, 1)  # outward surface normal
        else:
            n = (0, -1, 0)  # outward surface normal
        hn = (0, np.sin(alpha), np.cos(alpha))  # outward Bragg normal
        gamma0 = sum(i*j for i, j in zip(n, s0))
        gammah = sum(i*j for i, j in zip(n, sh))
        hns0 = sum(i*j for i, j in zip(hn, s0))

        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.88)
        ax = fig.add_subplot(111)

        curS, curP = crystal.get_amplitude(E, gamma0, gammah, hns0)
        curSD, curPD = crystal.get_amplitude_TT(E, gamma0, gammah, hns0,
                                             ucl=matCL, alphaAsym=alpha,
                                             Rcurvmm=Rcurv)

# phases:
#        ax2 = ax.twinx()
#        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
#        phi = np.unwrap(np.angle(curS * curP.conj()))
#        phiD = np.unwrap(np.angle(curSD * curPD.conj()))
#        p9, = ax2.plot((theta-thetaCenter) * convFactor, phi, 'c', lw=1,
#                       yunits=math.pi, zorder=0)
#        p10, = ax2.plot((theta-thetaCenter) * convFactor, -phiD, 'm', lw=1,
#                        yunits=math.pi, zorder=0)
#        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
#        ax2.yaxis.set_major_formatter(formatter)
#        for tl in ax2.get_yticklabels():
#            tl.set_color('c')

        if t is not None:
            tt = u', t={0:.0f}µm'.format(t * 1e3)
            tname = '{0:03d}mkm'.format(int(t * 1e3))
        else:
            tt = ' thick'
            tname = 'thick'
        if geom.startswith('Bragg'):
            geomPrefix = 'b'
        else:
            geomPrefix = 'l'
        if geom.endswith('transmitted'):
            geomPrefix += 't'
        if np.isinf(Rcurv):
            fig.suptitle(r'{0} Si{1}, $\alpha={2:.1f}^\circ$, bending R=$\infty$, E={3:.0f}keV'.format(geom, # analysis:ignore
                         hkl, alphaDeg, E0/1e3), fontsize=16)
        else:
            fig.suptitle(r'{0} Si{1}, $\alpha={2:.1f}^\circ$, bending R={3:.1f}m, E={4:.0f}keV'.format(geom, # analysis:ignore
                         hkl, alphaDeg, Rcurv/1e3, E0/1e3), fontsize=16)

        path = os.path.join('', 'XOP-RockingCurves-Bent') + os.sep
        if np.isinf(Rcurv) or alphaDeg == 0:
            x, R2p, R2s = np.loadtxt(
                "{0}{1}Si{2}_E{3:-.0f}keV_t{4}_R{5:-.0f}m_a{6:-.0f}deg.xc.gz".format( # analysis:ignore
                    path, geomPrefix, hkl, E0/1e3, tname, Rcurv/1e3, alphaDeg),
                unpack=True, usecols=(0, 2, 3))
            p1, = ax.plot(x, R2s, '-k', label='s XCrystal', linewidth=2)
#            p2, = ax.plot(x, R2p, '--k', label='p XCrystal')

        if xcb_tt:
            x, R2s = np.loadtxt(
                "{0}{1}Si{2}_E{3:-.0f}keV_t{4}_R{5:-.0f}m_a{6:-.0f}deg_tt_sigma.xcb.gz".format( # analysis:ignore
                    path, geomPrefix, hkl, E0/1e3, tname, Rcurv/1e3, alphaDeg),
                unpack=True, usecols=(0, 3))
            p3t, = ax.plot(x*1e3, R2s, '-b', label='s XCrystal_Bent TT')
            x, R2p = np.loadtxt(
                "{0}{1}Si{2}_E{3:-.0f}keV_t{4}_R{5:-.0f}m_a{6:-.0f}deg_tt_pi.xcb.gz".format( # analysis:ignore
                    path, geomPrefix, hkl, E0/1e3, tname, Rcurv/1e3, alphaDeg),
                unpack=True, usecols=(0, 3))
    #        p4, = ax.plot(x*1e3, R2p, '--b', label='p XCrystal_Bent TT')
        if xcb_pp:
            x, R2s = np.loadtxt(
                "{0}{1}Si{2}_E{3:-.0f}keV_t{4}_R{5:-.0f}m_a{6:-.0f}deg_pp_sigma.xcb.gz".format( # analysis:ignore
                    path, geomPrefix, hkl, E0/1e3, tname, Rcurv/1e3, alphaDeg),
                unpack=True, usecols=(0, 7))
            p3p, = ax.plot(x*1e3, R2s, '-c', label='s XCrystal_Bent PP')
            x, R2p = np.loadtxt(
                "{0}{1}Si{2}_E{3:-.0f}keV_t{4}_R{5:-.0f}m_a{6:-.0f}deg_pp_pi.xcb.gz".format( # analysis:ignore
                    path, geomPrefix, hkl, E0/1e3, tname, Rcurv/1e3, alphaDeg),
                unpack=True, usecols=(0, 7))
    #        p4, = ax.plot(x*1e3, R2p, '--b', label='p XCrystal_Bent TT')

#        if np.isinf(Rcurv) or alphaDeg == 0:
        p7, = ax.plot((theta - thetaCenter) * convFactor,
                      abs(curS)**2, '-r', linewidth=2)
#            p8, = ax.plot((theta - thetaCenter) * convFactor,
#                          abs(curP)**2, '-c', linewidth=2)
        p11, = ax.plot((theta - thetaCenter) * convFactor,
                       abs(curSD)**2, '--g', linewidth=2)
#        p12, = ax.plot((theta - thetaCenter) * convFactor,
#                       abs(curPD)**2, '--r')

        ax.set_xlabel(r'$\theta-\theta_B$ ($\mu$rad)')
        if geom.endswith('transmitted'):
            ax.set_ylabel('transmittivity')
        else:
            ax.set_ylabel('reflectivity')
        ax.set_xlim([dtheta[0] * convFactor, dtheta[-1] * convFactor])

        plotList = [p7, p11]
        curveList = ['xrt perfect', 'xrt TT']

        if np.isinf(Rcurv) or alphaDeg == 0:
            plotList.append(p1)
            curveList.append('XCrystal')
        if xcb_tt:
            plotList.append(p3t)
            curveList.append('XCrystal_Bent TT')
        if xcb_pp:
            plotList.append(p3p)
            curveList.append('XCrystal_Bent PP')
        legendPostmp = legendPos2 if alphaDeg > 0 else legendPos2+1
        ax.legend(plotList, curveList, loc=legendPostmp)
#        ax2.add_artist(l1)

        fname = '{0}Si{1}_{2}_a{3:-.0f}_{4:-.2f}'.format(
            geomPrefix, hkl, tname, alphaDeg, Rcurv/1e3)

        fig.savefig(fname + '.png')

    E0 = 50000.
#    convFactor = 180 / np.pi * 3600.  # arcsec
    convFactor = 1e6
    for alpha in alphas:
        if hkl == '111':  # Si111
            if geom.startswith('Bragg'):
                dtheta = np.linspace(0, 100, 400) * 1e-6
            else:
                dtheta = np.linspace(-5-np.abs(alpha)*2*50e3/Rcurvmm,
                                     5+np.abs(alpha)*2*50e3/Rcurvmm,
                                     1000) * 1e-6
            dSpacing = 3.13562
            hklInd = 1, 1, 1
        elif hkl == '333':  # Si333
            if geom.startswith('Bragg'):
                dtheta = np.linspace(-25, 75, 400) * 1e-6
            else:
                dtheta = np.linspace(-2-np.abs(alpha)**1.2*50e3/Rcurvmm,
                                     2+np.abs(alpha)**1.2*50e3/Rcurvmm,
                                     1000) * 1e-6
            dSpacing = 3.13562 / 3.
            hklInd = 3, 3, 3

        siCrystal = rm.CrystalDiamond(hklInd, dSpacing, t=t, geom=geom,
                                      factDW=factDW)
        thetaCenter = math.asin(rm.ch / (2*siCrystal.d*E0))

        E = np.ones_like(dtheta) * E0
        theta = dtheta + thetaCenter
        for_one_alpha(siCrystal, alpha, hkl)


def compare_Bragg_Laue(hkl, beamPath, factDW=1.):
    """A comparison subroutine used in the module test suit."""
    def for_one_alpha(alphaDeg, hkl):
        alpha = math.radians(alphaDeg)
        s0 = (np.zeros_like(theta), np.cos(theta+alpha), -np.sin(theta+alpha))
        sh = (np.zeros_like(theta), np.cos(theta-alpha), np.sin(theta-alpha))

#'Bragg':
        n = (0, 0, 1)  # outward surface normal
        hn = (0, math.sin(alpha), math.cos(alpha))  # outward Bragg normal
        gamma0 = sum(i*j for i, j in zip(n, s0))
        gammah = sum(i*j for i, j in zip(n, sh))
        hns0 = sum(i*j for i, j in zip(hn, s0))
        braggS, braggP = siBraggCrystal.get_amplitude(E, gamma0, gammah, hns0)
#'Laue':
        n = (0, -1, 0)  # outward surface normal
        hn = (0, math.sin(alpha), math.cos(alpha))  # outward Bragg normal
        gamma0 = sum(i*j for i, j in zip(n, s0))
        gammah = sum(i*j for i, j in zip(n, sh))
        hns0 = sum(i*j for i, j in zip(hn, s0))
        laueS, laueP = siLaueCrystal.get_amplitude(E, gamma0, gammah, hns0)

        fig = plt.figure(figsize=(8, 6), dpi=100)
        ax = fig.add_subplot(111)

# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(braggS * braggP.conj()))
        p5, = ax2.plot((theta-thetaCenter) * convFactor, phi, '-c', lw=1,
                       yunits=math.pi, zorder=0)
        phi = np.unwrap(np.angle(laueS * laueP.conj()))
        p6, = ax2.plot((theta-thetaCenter) * convFactor, phi, '-c.', lw=1,
                       yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')

        fig.suptitle(r'Comparison of Bragg and Laue transmittivity for Si{0}'.
                     format(hkl), fontsize=16)
        p1, = ax.plot((theta-thetaCenter) * convFactor, abs(braggS)**2, '-r')
        p2, = ax.plot((theta-thetaCenter) * convFactor, abs(braggP)**2, '-b')
        p3, = ax.plot((theta-thetaCenter) * convFactor, abs(laueS)**2, '-r.')
        p4, = ax.plot((theta-thetaCenter) * convFactor, abs(laueP)**2, '-b.')
        ax.set_xlabel(r'$\theta-\theta_B$ (arcsec)')
        ax.set_ylabel('transmittivity')

#upper right	1
#upper left	2
#lower left	3
#lower right	4
#right   	5
#center left	6
#center right	7
#lower center	8
#upper center	9
#center         10
        l1 = ax.legend([p1, p2], ['s', 'p'], loc=3)
        ax.legend([p1, p3], [u'Bragg t={0:.1f} µm'.format(
            siBraggCrystal.t * 1e3), u'Laue t={0:.1f} µm'.format(
            siLaueCrystal.t * 1e3)], loc=2)
        ax.add_artist(l1)
        ax.set_xlim([dtheta[0] * convFactor, dtheta[-1] * convFactor])

        fname = r'BraggLaueTrSi{0}'.format(hkl)
        fig.savefig(fname + '.png')

    E0 = 10000.
    convFactor = 180 / math.pi * 3600.  # arcsec
    if hkl == '111':  # Si111
        dtheta = np.linspace(-100, 100, 400) * 1e-6
        dSpacing = 3.13562
        hklInd = 1, 1, 1
    elif hkl == '333':  # Si333
        dtheta = np.linspace(-30, 30, 400) * 1e-6
        dSpacing = 3.13562 / 3
        hklInd = 3, 3, 3

    thetaCenter = math.asin(rm.ch / (2*dSpacing*E0))
    t = beamPath * math.sin(thetaCenter)
    siBraggCrystal = rm.CrystalDiamond(hklInd, dSpacing, t=t,
                                       geom='Bragg transmitted', factDW=factDW)
    t = beamPath * math.cos(thetaCenter)
    siLaueCrystal = rm.CrystalDiamond(hklInd, dSpacing, t=t,
                                      geom='Laue transmitted', factDW=factDW)

    E = np.ones_like(dtheta) * E0
    theta = dtheta + thetaCenter
    for_one_alpha(0., hkl)
#    for_one_alpha(siCrystal, -5., hkl)
#    for_one_alpha(siCrystal, 5., hkl)


def compare_reflectivity():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(stripe, refs, refp, theta, reprAngle):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.86)
        ax = fig.add_subplot(111)
        ax.set_xlabel('energy (eV)')
        ax.set_ylabel('reflectivity')
        ax.set_xlim(30, 5e4)
        fig.suptitle(stripe.name + ' ' + reprAngle, fontsize=16)
        x, R2s = np.loadtxt(refs, unpack=True)
        p1, = ax.plot(x, R2s, '-k', label='s xf1f2')
        x, R2s = np.loadtxt(refp, unpack=True)
        p2, = ax.plot(x, R2s, '--k', label='p xf1f2')
        refl = stripe.get_amplitude(E, math.sin(theta))
        rs, rp = refl[0], refl[1]
        p3, = ax.semilogx(E, abs(rs)**2, '-r')
        p4, = ax.semilogx(E, abs(rp)**2, '--r')
        l1 = ax.legend([p1, p2], ['s', 'p'], loc=3)
        ax.legend([p1, p3], ['Xf1f2/XOP', 'xrt'], loc=6)
        ax.add_artist(l1)
# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(rs * rp.conj()))
        p9, = ax2.plot(E, phi, 'c', lw=2, yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')

        fname = 'MirrorRefl' + stripe.name + "".join(reprAngle.split())
        fig.savefig(fname + '.png')

    dataDir = os.path.join('', 'XOP-Reflectivities')
    E = np.logspace(1.+math.log10(3.), 4.+math.log10(5.), 500)
    stripeSi = rm.Material('Si', rho=2.33)
    for_one_material(stripeSi,
                     os.path.join(dataDir, "Si05deg_s.xf1f2.gz"),
                     os.path.join(dataDir, "Si05deg_p.xf1f2.gz"),
                     math.radians(0.5), '@ 0.5 deg')
    stripePt = rm.Material('Pt', rho=21.45)
    for_one_material(stripePt,
                     os.path.join(dataDir, "Pt4mrad_s.xf1f2.gz"),
                     os.path.join(dataDir, "Pt4mrad_p.xf1f2.gz"),
                     4e-3, '@ 4 mrad')
    stripeSiO2 = rm.Material(('Si', 'O'), quantities=(1, 2), rho=2.2)
    for_one_material(stripeSiO2,
                     os.path.join(dataDir, "SiO205deg_s.xf1f2.gz"),
                     os.path.join(dataDir, "SiO205deg_p.xf1f2.gz"),
                     math.radians(0.5), '@ 0.5 deg')
    stripeRh = rm.Material('Rh', rho=12.41)
    for_one_material(stripeRh,
                     os.path.join(dataDir, "Rh2mrad_s.xf1f2.gz"),
                     os.path.join(dataDir, "Rh2mrad_p.xf1f2.gz"),
                     2e-3, '@ 2 mrad')


def compare_reflectivity_coated():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(stripe, strOnly, refs, refp, theta, reprAngle):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.86)
        ax = fig.add_subplot(111)
        ax.set_xlabel('energy (keV)')
        ax.set_ylabel('reflectivity')
        # ax.set_xlim(100, 4e4)
        ax.set_ylim(1e-7, 2)
        fig.suptitle(stripe.name + ' ' + reprAngle, fontsize=16)
        x, R2s = np.loadtxt(refs, unpack=True, skiprows=2, usecols=(0, 1))
        p1, = ax.semilogy(x*1e-3, R2s, '-k', label='s CXRO')
        x, R2s = np.loadtxt(refp, unpack=True, skiprows=2, usecols=(0, 1))
        p2, = ax.semilogy(x*1e-3, R2s, '--k', label='p CXRO')
        refl = stripe.get_amplitude(E, math.sin(theta))
        rs, rp = refl[0], refl[1]
        rs0, rp0 = strOnly.get_amplitude(E, math.sin(theta))[0:2]
        p3, = ax.semilogy(E*1e-3, abs(rs)**2, '-r')
        p4, = ax.semilogy(E*1e-3, abs(rp)**2, '--r')
        p5, = ax.semilogy(E*1e-3, abs(rs0)**2, '-m')
        p6, = ax.semilogy(E*1e-3, abs(rp0)**2, '--c')
        l1 = ax.legend([p1, p2], ['s', 'p'], loc=3)
        ax.legend([p1, p3, p5], ['CXRO', 'xrt', 'bulk coating'], loc=1)
        ax.add_artist(l1)
# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(rs * rp.conj()))
        p9, = ax2.plot(E*1e-3, phi, 'c', lw=2, yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')

        ax2.set_zorder(-1)
        ax.patch.set_visible(False)  # hide the 'canvas'

        fname = 'MirrorRefl' + stripe.name + "".join(reprAngle.split())
        fig.savefig(fname + '.png')

    dataDir = os.path.join('', 'CXRO-Reflectivities')
    E = np.logspace(2., 4.+math.log10(4.), 1000)
    mSi = rm.Material('Si', rho=2.33)
    mSiO2 = rm.Material(('Si', 'O'), quantities=(1, 2), rho=2.65)
#    mB4C = rm.Material(('B', 'C'), quantities=(4, 1), rho=2.52)
    mRh = rm.Material('Rh', rho=12.41, kind='mirror')
    mC = rm.Material('C', rho=3.5, kind='mirror')
    cRhSi = rm.Coated(coating=mRh, cThickness=300,
                      substrate=mSi, surfaceRoughness=20,
                      substRoughness=20, name='30 nm Rh on Si')
    cCSiO2 = rm.Coated(coating=mC, cThickness=200,
                        substrate=mSiO2, surfaceRoughness=10,
                        substRoughness=10, name='20 nm Diamond on Quartz')
    for_one_material(cRhSi, mRh,
                     os.path.join(dataDir, "RhSi_s_rough2.CXRO.gz"),
                     os.path.join(dataDir, "RhSi_p_rough2.CXRO.gz"),
                     4e-3, '@ 4 mrad,\nRMS roughness 2 nm')

    for_one_material(cCSiO2, mC,
                      os.path.join(dataDir, "CSiO2_s_rough1.CXRO.gz"),
                      os.path.join(dataDir, "CSiO2_p_rough1.CXRO.gz"),
                      np.radians(0.2), '@ 0.2 deg,\nRMS roughness 1 nm')


def compare_reflectivity_slab():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(stripe, refs, refp, E, reprEnergy):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.86)
        ax = fig.add_subplot(111)
        ax.set_xlabel('grazing angle (deg)')
        ax.set_ylabel('reflectivity')
        ax.set_xlim(0, 10)
        fig.suptitle(stripe.name + ' ' + reprEnergy, fontsize=16)
        x, R2s = np.loadtxt(refs, unpack=True)
        p1, = ax.plot(x, R2s, '-k', label='s Mlayer')
        x, R2s = np.loadtxt(refp, unpack=True)
        p2, = ax.plot(x, R2s, '--k', label='p Mlayer')
        refl = stripe.get_amplitude(E, np.sin(np.deg2rad(theta)))
        rs, rp = refl[0], refl[1]
        p3, = ax.semilogy(theta, abs(rs)**2, '-r')
        p4, = ax.semilogy(theta, abs(rp)**2, '--r')
        l1 = ax.legend([p1, p2], ['s', 'p'], loc=3)
        ax.legend([p1, p3], ['Mlayer/XOP', 'xrt'], loc=1)
        ax.add_artist(l1)
        ylim = ax.get_ylim()
        ax.set_ylim([ylim[0], 1])
# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(rs * rp.conj()))
        p9, = ax2.plot(theta, phi, 'c', lw=2, yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')

        ax2.set_zorder(-1)
        ax.patch.set_visible(False)  # hide the 'canvas'

        fname = 'SlabRefl' + stripe.name + ' ' + reprEnergy
        fig.savefig(fname + '.png')

    dataDir = os.path.join('', 'XOP-Reflectivities')
    theta = np.linspace(0, 10, 500)  # degrees
    layerW = rm.Material('W', kind='thin mirror', rho=19.3, t=2.5e-6)
    for_one_material(layerW,
                     os.path.join(dataDir, "W25A_10kev_s.mlayer.gz"),
                     os.path.join(dataDir, "W25A_10kev_p.mlayer.gz"), 1e4,
                     u'slab, t = 25 Å, @ 10 keV')


def compare_reflectivity_multilayer():
    """A comparison subroutine used in the module test suit."""
#    cl_list = None
    try:
        import pyopencl as cl
        os.environ['PYOPENCL_COMPILER_OUTPUT'] = '1'
        isOpenCL = True
    except ImportError:
        isOpenCL = False

    if isOpenCL:
        import xrt.backends.raycing.myopencl as mcl
        matCL = mcl.XRT_CL(r'materials.cl')
#        cl_list = matCL.cl_ctx[0], matCL.cl_queue[0], matCL.cl_program[0]
    else:
        matCL = None

    def for_one_material(ml, refs, E, label, flabel=''):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.86)
        ax = fig.add_subplot(111)
        ax.set_xlabel('grazing angle (deg)')
        ax.set_ylabel('reflectivity')
        ax.set_xlim(theta[0], theta[-1])
        fig.suptitle(label, fontsize=14)
        x, R2s = np.loadtxt(refs, unpack=True)
        p1, = ax.plot(x, R2s, '-k', label='s Mlayer')
        refl = ml.get_amplitude(E, np.sin(np.deg2rad(theta)), ucl=matCL)
        rs, rp = refl[0], refl[1]
        p3, = ax.plot(theta, abs(rs)**2, '-r', lw=1)
        p4, = ax.plot(theta, abs(rp)**2, '--r')
        l1 = ax.legend([p3, p4], ['s', 'p'], loc=3)
        ax.legend([p1, p3], ['Mlayer/XOP', 'xrt'], loc=1)
        ax.add_artist(l1)
        ylim = ax.get_ylim()
        ax.set_ylim([ylim[0], 1])
# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(rs * rp.conj()))
        p9, = ax2.plot(theta, phi, 'c', lw=1, yunits=math.pi, zorder=0)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')
        ax2.set_xlim(theta[0], theta[-1])

        ax2.set_zorder(-1)
        ax.patch.set_visible(False)  # hide the 'canvas'

        fname = 'Multilayer' + ml.tLayer.name + ml.bLayer.name
        fig.savefig(fname + flabel)

    dataDir = os.path.join('', 'XOP-Reflectivities')
    theta = np.linspace(0, 1.6, 801)  # degrees
    mSi = rm.Material('Si', rho=2.33)
    mW = rm.Material('W', rho=19.3)

    mL = rm.Multilayer(mSi, 27, mW, 18, 40, mSi)
    for_one_material(mL, os.path.join(dataDir, "WSi45A04.mlayer.gz"), 8050,
                     u'40 × [27 Å Si + 18 Å W] multilayer @ 8.05 keV')

    mL = rm.Multilayer(mSi, 27*2, mW, 18*2, 40, mSi, 27, 18, 2)
    for_one_material(mL, os.path.join(dataDir, "WSi45_100A40.mlayer.gz"), 8050,
                     u'Depth graded multilayer \n 40 × [54 Å Si + 36 Å W]'
                     u' to [27 Å Si + 18 Å W] @ 8.05 keV', '-graded')

#    mL = rm.Multilayer(mSi, 27, mW, 18, 40, mSi, 27*2, 18*2, 2)
#    for_one_material(mL, os.path.join(dataDir, "WSi100_45A40.mlayer.gz"), 8050,
#                     u'Depth graded multilayer \n 40 × [27 Å Si + 18 Å W]'
#                     u' to [54 Å Si + 36 Å W] multilayer @ 8.05 keV',
#                     '-antigraded')


def compare_reflectivity_multilayer_interdiffusion():
    """A comparison subroutine used in the module test suit."""
#    cl_list = None
    try:
        import pyopencl as cl
        os.environ['PYOPENCL_COMPILER_OUTPUT'] = '1'
        isOpenCL = True
    except ImportError:
        isOpenCL = False

    if isOpenCL:
        import xrt.backends.raycing.myopencl as mcl
        matCL = mcl.XRT_CL(r'materials.cl')
#        cl_list = matCL.cl_ctx[0], matCL.cl_queue[0], matCL.cl_program[0]
    else:
        matCL = None

    def for_one_material(ml, refs, E, label, flabel=''):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        fig.subplots_adjust(right=0.86)
        ax = fig.add_subplot(111)
        ax.set_xlabel('grazing angle (deg)')
        ax.set_ylabel('reflectivity')
        ax.set_xlim(theta[0], theta[-1])
        fig.suptitle(label, fontsize=14)

        x, R2s = np.loadtxt(refs, unpack=True, skiprows=2, usecols=(0, 1))
        refl = ml.get_amplitude(E, np.sin(np.deg2rad(theta)), ucl=matCL)
        rs, rp = refl[0], refl[1]

# amplitudes:
        p1, = ax.plot(x, R2s, '-k', label='s CXRO')
        p3, = ax.plot(theta, abs(rs)**2, '-r', lw=1)
        p4, = ax.plot(theta, abs(rp)**2, '--r')
        l1 = ax.legend([p3, p4], ['s', 'p'], loc=3)
        ax.legend([p1, p3], ['CXRO-Multilayer', 'xrt'], loc=1)
        ax.add_artist(l1)
        ylim = ax.get_ylim()
        ax.set_ylim([ylim[0], 1])

# phases:
        ax2 = ax.twinx()
        ax2.set_ylabel(r'$\phi_s - \phi_p$', color='c')
        phi = np.unwrap(np.angle(rs * rp.conj()))
        p9, = ax2.plot(theta, phi, 'c', lw=1, yunits=math.pi)
        ax2.set_ylim(-0.001, 0.001)
        formatter = mpl.ticker.FormatStrFormatter('%g' + r'$ \pi$')
        ax2.yaxis.set_major_formatter(formatter)
        for tl in ax2.get_yticklabels():
            tl.set_color('c')
        ax2.set_xlim(theta[0], theta[-1])

        ax2.set_zorder(-1)
        ax.patch.set_visible(False)  # hide the 'canvas'

        fname = 'Multilayer' + ml.tLayer.name + ml.bLayer.name
        fig.savefig(fname + flabel)

    dataDir = os.path.join('', 'CXRO-Reflectivities')
    theta = np.linspace(0, 1.6, 1001)  # degrees
    mSi = rm.Material('Si', rho=2.33)
    mW = rm.Material('W', rho=19.3)

    mL = rm.Multilayer(mSi, 17.82, mW, 11.88, 300, mSi, idThickness=0)
    for_one_material(mL, os.path.join(dataDir, "WSi300id0.CXRO.gz"), 24210,
                     u'300 × [17.82 Å Si + 11.88 Å W] multilayer @ 24.21 keV\nInterdiffusion RMS 0 Å',
                     'CXRO_id0')

    mL = rm.Multilayer(mSi, 17.82, mW, 11.88, 300, mSi, idThickness=6)
    for_one_material(mL, os.path.join(dataDir, "WSi300id6.CXRO.gz"), 24210,
                     u'300 × [17.82 Å Si + 11.88 Å W] multilayer @ 24.21 keV\nInterdiffusion RMS 6 Å',
                     'CXRO_id6')


def compare_dTheta():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(mat, ref1, title):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        ax = fig.add_subplot(111)
        ax.set_xlabel(r'$\theta_{B}-\alpha$, deg')
        ax.set_ylabel(r'$\delta\theta$, deg')
        fig.suptitle(title, fontsize=16)
        thetaB = np.degrees(mat.get_Bragg_angle(E[0]))
        calc_dt_new = np.degrees(
            np.abs(mat.get_dtheta(E, np.radians(alpha))))
        p2, = ax.semilogy(
            alpha+thetaB, calc_dt_new, '-b',
            label=r'with curvature')
        calc_dt_reg = np.degrees(
            np.abs(mat.get_dtheta_regular(E, np.radians(alpha))))
        p3, = ax.semilogy(
            alpha+thetaB, calc_dt_reg, '-r',
            label=r'without curvature')
        ax.legend(loc=0)
        ax.set_xlim(0, 90)
        ax.set_ylim(6e-5, 0.3)
        fname = title
        fig.savefig(fname + '.png')

    E = np.ones(500) * 10000.
    alpha = np.linspace(-90., 90., 500)
    mat = rm.CrystalSi(tK=80)
    titleStr = u'Deviation from the Bragg angle, Si(111), {0:d}keV'.format(
        int(E[0]/1000))
    for_one_material(mat, None, titleStr)


def compare_absorption_coeff():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(m):
        rf = os.path.join(dataDir, "{0}_absCoeff.xcrosssec.gz".format(m.name))
        title = u'Absorption in {0}'.format(mat.name)
        fig = plt.figure(figsize=(8, 6), dpi=100)
        ax = fig.add_subplot(111)
        ax.set_xlabel('energy (eV)')
        ax.set_ylabel(r'$\mu_0$ (cm$^{-1}$)')
        fig.suptitle(title, fontsize=16)
        x, mu0 = np.loadtxt(rf, unpack=True)
        p1, = ax.loglog(x, mu0, '-k', lw=2, label='XCrossSec')
        calcmu0 = m.get_absorption_coefficient(E)
        p3, = ax.loglog(E, calcmu0, '-r', label='xrt')
        ax.legend(loc=1)
        ax.set_xlim(E[0], E[-1])
        fname = title
        fig.savefig(fname + '.png')

    dataDir = os.path.join('', 'XOP-Reflectivities')
    E = np.logspace(1+math.log10(2.), 4.+math.log10(3.), 500)

#    mat = rm.Material('Be', rho=1.848)
#    for_one_material(mat)
#    mat = rm.Material('Ag', rho=10.50)
#    mat = rm.Material('Ag', rho=10.50, table='Henke')
#    for_one_material(mat)
    mat = rm.Material('Al', rho=2.6989)
    for_one_material(mat)
#    mat = rm.Material('Au', rho=19.3)
#    for_one_material(mat)
#    mat = rm.Material('Ni', rho=8.902)
#    for_one_material(mat)
    E = 30000
    print("abs coeff at {0} keV = {1} 1/cm".format(
        E*1e-3, mat.get_absorption_coefficient(E)))
    print("refr index at {0} keV = {1}".format(
        E*1e-3, mat.get_refractive_index(E)))
#    el = rm.Element('Ag')
#    print("f1, f2", el.get_f1f2(30000))


def compare_transmittivity():
    """A comparison subroutine used in the module test suit."""
    def for_one_material(mat, thickness, ref1, title, sname):
        fig = plt.figure(figsize=(8, 6), dpi=100)
        ax = fig.add_subplot(111)
        ax.set_xlabel('energy (eV)')
        ax.set_ylabel('transmittivity')
        fig.suptitle(title, fontsize=16)
        x, tr = np.loadtxt(ref1, unpack=True)
        p1, = ax.semilogx(x, tr, '-k', lw=2, label='XPower/XOP')
        calcmu0 = mat.get_absorption_coefficient(E)
        transm = np.exp(-calcmu0 * thickness)
        p3, = ax.semilogx(E, transm, '-r', label='xrt')
        ax.legend(loc=2)
        ax.set_xlim(E[0], E[-1])
        fname = 'Transm' + sname
        fig.savefig(fname + '.png')

    dataDir = os.path.join('', 'XOP-Reflectivities')
    E = np.logspace(2.+math.log10(3.), 4.+math.log10(3.), 500)
    matDiamond = rm.Material('C', rho=3.52)
    for_one_material(matDiamond, 60*1e-4,
                     os.path.join(dataDir, "Diamond60mum.xpower.gz"),
                     r'Transmittivity of 60-$\mu$m-thick diamond', 'Diamond')


def run_tests():
    """The body of the module test suit. Uncomment the tests you want."""

#Compare the calculated rocking curves of Si crystals with those calculated by
#XCrystal and XInpro (parts of XOP):
    compare_rocking_curves('111')
    # compare_rocking_curves('333')
    # compare_rocking_curves('111', t=0.007)  # t is thickness in mm
    # compare_rocking_curves('333', t=0.007)
    # compare_rocking_curves('111', t=0.100)
    # compare_rocking_curves('333', t=0.100)
    compare_rocking_curves('111', t=0.007, geom='Bragg transmitted')
    # compare_rocking_curves('333', t=0.007, geom='Bragg transmitted')
    # compare_rocking_curves('111', t=0.100, geom='Bragg transmitted')
    # compare_rocking_curves('333', t=0.100, geom='Bragg transmitted')
    # compare_rocking_curves('111', t=0.007, geom='Laue reflected')
    # compare_rocking_curves('333', t=0.007, geom='Laue reflected')
    # compare_rocking_curves('111', t=0.100, geom='Laue reflected')
    # compare_rocking_curves('333', t=0.100, geom='Laue reflected')
    # compare_rocking_curves('111', t=0.007, geom='Laue transmitted')
    # compare_rocking_curves('333', t=0.007, geom='Laue transmitted')
    # compare_rocking_curves('111', t=0.100, geom='Laue transmitted')
    # compare_rocking_curves('333', t=0.100, geom='Laue transmitted')

# Compare rocking curves for bent Si crystals with those calculated by
#XCrystal_Bent (Takagi-Taupin):
    compare_rocking_curves_bent('111', t=1.0, geom='Laue reflected',
                          Rcurvmm=np.inf, alphas=[30])
    # compare_rocking_curves_bent('333', t=1.0, geom='Laue reflected',
    #                       Rcurvmm=np.inf, alphas=[30])
    # compare_rocking_curves_bent('111', t=1.0, geom='Laue reflected',
    #                       Rcurvmm=50*1e3,
    #                       alphas=[-60, -45, -30, -15, 0, 15, 30, 45, 60])
    # compare_rocking_curves_bent('333', t=1.0, geom='Laue reflected',
    #                       Rcurvmm=50*1e3,
    #                       alphas=[-60, -45, -30, -15, 0, 15, 30, 45, 60])


#check that Bragg transmitted and Laue transmitted give the same results if the
#beam path is equal:
    beamPath = 0.1  # mm
    compare_Bragg_Laue('111', beamPath=beamPath)
    compare_Bragg_Laue('333', beamPath=beamPath)

#Compare the calculated reflectivities of Si, Pt, SiO_2 with those by Xf1f2
#(part of XOP):
    compare_reflectivity()

    compare_reflectivity_coated()

#Compare the calculated reflectivities of W slab with those by Mlayer
#(part of XOP):
    compare_reflectivity_slab()

#Compare the calculated reflectivities of W slab with those by Mlayer
#(part of XOP):
    # compare_reflectivity_multilayer()
    compare_reflectivity_multilayer_interdiffusion()
    # compare_dTheta()

#Compare the calculated absorption coefficient with that by XCrossSec
#(part of XOP):
    compare_absorption_coeff()

#Compare the calculated transmittivity with that by XPower
#(part of XOP):
    compare_transmittivity()

#Play with Si crystal:
    crystalSi = rm.CrystalSi(hkl=(1, 1, 1), tK=100.)
    print(2 * crystalSi.get_a()/math.sqrt(3.))  # 2dSi111
    print('Si111 d-spacing = {0:.6f}'.format(crystalSi.d))
    print(crystalSi.get_Bragg_offset(8600, 8979))

    crystalDiamond = rm.CrystalDiamond((1, 1, 1), 2.0592872, elements='C')
    E = 9000.
    print(u'Darwin width at E={0:.0f} eV is {1:.5f} µrad for s-polarization'.
          format(E, crystalDiamond.get_Darwin_width(E) * 1e6))
    print(u'Darwin width at E={0:.0f} eV is {1:.5f} µrad for p-polarization'.
          format(E, crystalDiamond.get_Darwin_width(E, polarization='p')*1e6))

    plt.show()
    print("finished")


if __name__ == '__main__':
    run_tests()
