def latticeVectors(lparms, tag="cubic", radians=False, debug=False):
"""
Generates direct and reciprocal lattice vector components in a
crystal-relative RHON basis, X. The convention for fixing X to the
lattice is such that a || x1 and c* || x3, where a and c* are
direct and reciprocal lattice vectors, respectively.
USAGE:
lattice = LatticeVectors(lparms, <symmTag>)
INPUTS:
1) lparms (1 x n float list) is the array of lattice parameters,
where n depends on the symmetry group (see below).
2) symTag (string) is a case-insensitive string representing the
symmetry type of the implied Laue group. The 11 available choices
are shown below. The default value is 'cubic'. Note that each
group expects a lattice parameter array of the indicated length
and order.
latticeType lparms
----------- ------------
'cubic' a
'hexagonal' a, c
'trigonal' a, c
'rhombohedral' a, alpha (in degrees)
'tetragonal' a, c
'orthorhombic' a, b, c
'monoclinic' a, b, c, beta (in degrees)
'triclinic' a, b, c, alpha, beta, gamma (in degrees)
OUTPUTS:
1) lattice is a dictionary containing the following keys/items:
F (3, 3) double array transformation matrix taking
componenents in the direct
lattice (i.e. {uvw}) to the
reference, X
B (3, 3) double array transformation matrix taking
componenents in the reciprocal
lattice (i.e. {hkl}) to X
BR (3, 3) double array transformation matrix taking
componenents in the reciprocal
lattice to the Fable reference
frame (see notes)
U0 (3, 3) double array transformation matrix
(orthogonal) taking
componenents in the
Fable reference frame to X
vol double the unit cell volume
dparms (6, ) double list the direct lattice parameters:
[a b c alpha beta gamma]
rparms (6, ) double list the reciprocal lattice
parameters:
[a* b* c* alpha* beta* gamma*]
NOTES:
*) The conventions used for assigning a RHON basis,
X -> {x1, x2, x3}, to each point group are consistent with
those published in Appendix B of [1]. Namely: a || x1 and
c* || x3. This differs from the convention chosen by the Fable
group, where a* || x1 and c || x3 [2].
*) The unit cell angles are defined as follows:
alpha=acos(b'*c/|b||c|), beta=acos(c'*a/|c||a|), and
gamma=acos(a'*b/|a||b|).
*) The reciprocal lattice vectors are calculated using the
crystallographic convention, where the prefactor of 2*pi is
omitted. In this convention, the reciprocal lattice volume is
1/V.
*) Several relations from [3] were employed in the component
calculations.
REFERENCES:
[1] J. F. Nye, ``Physical Properties of Crystals: Their
Representation by Tensors and Matrices''. Oxford University
Press, 1985. ISBN 0198511655
[2] E. M. Lauridsen, S. Schmidt, R. M. Suter, and H. F. Poulsen,
``Tracking: a method for structural characterization of grains
in powders or polycrystals''. J. Appl. Cryst. (2001). 34,
744--750
[3] R. J. Neustadt, F. W. Cagle, Jr., and J. Waser, ``Vector
algebra and the relations between direct and reciprocal
lattice quantities''. Acta Cryst. (1968), A24, 247--248
"""
# build index for sorting out lattice parameters
lattStrings = [
"cubic",
"hexagonal",
"trigonal",
"rhombohedral",
"tetragonal",
"orthorhombic",
"monoclinic",
"triclinic",
]
if radians:
angConv = 1.0
else:
angConv = pi / 180.0 # degToRad
deg90 = pi / 2.0
deg120 = 2.0 * pi / 3.0
#
if tag == lattStrings[0]: # cubic
cellparms = num.r_[num.tile(lparms[0], (3,)), deg90 * num.ones((3,))]
elif tag == lattStrings[1] or tag == lattStrings[2]: # hexagonal | trigonal (hex indices)
cellparms = num.r_[lparms[0], lparms[0], lparms[1], deg90, deg90, deg120]
elif tag == lattStrings[3]: # rhombohedral
cellparms = num.r_[num.tile(lparms[0], (3,)), num.tile(angConv * lparms[1], (3,))]
elif tag == lattStrings[4]: # tetragonal
cellparms = num.r_[lparms[0], lparms[0], lparms[1], deg90, deg90, deg90]
elif tag == lattStrings[5]: # orthorhombic
cellparms = num.r_[lparms[0], lparms[1], lparms[2], deg90, deg90, deg90]
elif tag == lattStrings[6]: # monoclinic
cellparms = num.r_[lparms[0], lparms[1], lparms[2], deg90, angConv * lparms[3], deg90]
elif tag == lattStrings[7]: # triclinic
cellparms = num.r_[
lparms[0], lparms[1], lparms[2], angConv * lparms[3], angConv * lparms[4], angConv * lparms[5]
] # fixed DP 2/24/16
else:
raise RuntimeError("lattice tag '%s' is not recognized" % (tag))
if debug:
print str(cellparms[0:3]) + " " + str(r2d * cellparms[3:6])
alfa = cellparms[3]
beta = cellparms[4]
gama = cellparms[5]
cosalfar, sinalfar = cosineXform(alfa, beta, gama)
a = cellparms[0] * num.r_[1, 0, 0]
b = cellparms[1] * num.r_[num.cos(gama), num.sin(gama), 0]
c = cellparms[2] * num.r_[num.cos(beta), -cosalfar * num.sin(beta), sinalfar * num.sin(beta)]
ad = num.sqrt(sum(a ** 2))
bd = num.sqrt(sum(b ** 2))
cd = num.sqrt(sum(c ** 2))
# Cell volume
V = num.dot(a, num.cross(b, c))
# F takes components in the direct lattice to X
F = num.c_[a, b, c]
# Reciprocal lattice vectors
astar = num.cross(b, c) / V
bstar = num.cross(c, a) / V
cstar = num.cross(a, b) / V
# and parameters
ar = num.sqrt(sum(astar ** 2))
br = num.sqrt(sum(bstar ** 2))
cr = num.sqrt(sum(cstar ** 2))
alfar = num.arccos(num.dot(bstar, cstar) / br / cr)
betar = num.arccos(num.dot(cstar, astar) / cr / ar)
gamar = num.arccos(num.dot(astar, bstar) / ar / br)
# B takes components in the reciprocal lattice to X
B = num.c_[astar, bstar, cstar]
cosalfar2, sinalfar2 = cosineXform(alfar, betar, gamar)
afable = ar * num.r_[1, 0, 0]
bfable = br * num.r_[num.cos(gamar), num.sin(gamar), 0]
cfable = cr * num.r_[num.cos(betar), -cosalfar2 * num.sin(betar), sinalfar2 * num.sin(betar)]
BR = num.c_[afable, bfable, cfable]
U0 = num.dot(B, num.linalg.inv(BR))
if outputDegrees:
dparms = num.r_[ad, bd, cd, r2d * num.r_[alfa, beta, gama]]
rparms = num.r_[ar, br, cr, r2d * num.r_[alfar, betar, gamar]]
else:
dparms = num.r_[ad, bd, cd, num.r_[alfa, beta, gama]]
rparms = num.r_[ar, br, cr, num.r_[alfar, betar, gamar]]
L = {"F": F, "B": B, "BR": BR, "U0": U0, "vol": V, "dparms": dparms, "rparms": rparms}
return L
def getFriedelPair(tth0, eta0, *ome0, **kwargs):
"""
Get the diffractometer angular coordinates in degrees for
the Friedel pair of a given reflection (min angular distance).
AUTHORS:
J. V. Bernier -- 10 Nov 2009
USAGE:
ome1, eta1 = getFriedelPair(tth0, eta0, *ome0,
display=False,
units='degrees',
convention='hexrd')
INPUTS:
1) tth0 is a list (or ndarray) of 1 or n the bragg angles (2theta) for
the n reflections (tiled to match eta0 if only 1 is given).
2) eta0 is a list (or ndarray) of 1 or n azimuthal coordinates for the n
reflections (tiled to match tth0 if only 1 is given).
3) ome0 is a list (or ndarray) of 1 or n reference oscillation
angles for the n reflections (denoted omega in [1]). This argument
is optional.
4) Keyword arguments may be one of the following:
Keyword Values|{default} Action
-------------- -------------- --------------
'display' True|{False} toggles display info to cmd line
'units' 'radians'|{'degrees'} sets units for input angles
'convention' 'fable'|{'hexrd'} sets conventions defining
the angles (see below)
'chiTilt' None the inclination (about Xlab) of
the oscillation axis
OUTPUTS:
1) ome1 contains the oscialltion angle coordinates of the
Friedel pairs associated with the n input reflections, relative to ome0
(i.e. ome1 = <result> + ome0). Output is in DEGREES!
2) eta1 contains the azimuthal coordinates of the Friedel
pairs associated with the n input reflections. Output units are
controlled via the module variable 'outputDegrees'
NOTES:
JVB) The ouputs ome1, eta1 are written using the selected convention, but the
units are alway degrees. May change this to work with Nathan's global...
JVB) In the 'fable' convention [1], {XYZ} form a RHON basis where X is
downstream, Z is vertical, and eta is CCW with +Z defining eta = 0.
JVB) In the 'hexrd' convention [2], {XYZ} form a RHON basis where Z is upstream,
Y is vertical, and eta is CCW with +X defining eta = 0.
REFERENCES:
[1] E. M. Lauridsen, S. Schmidt, R. M. Suter, and H. F. Poulsen,
``Tracking: a method for structural characterization of grains in
powders or polycrystals''. J. Appl. Cryst. (2001). 34, 744--750
[2] J. V. Bernier, M. P. Miller, J. -S. Park, and U. Lienert,
``Quantitative Stress Analysis of Recrystallized OFHC Cu Subject
to Deformed In Situ'', J. Eng. Mater. Technol. (2008). 130.
DOI:10.1115/1.2870234
"""
dispFlag = False
fableFlag = False
chi = None
c1 = 1.0
c2 = pi / 180.0
zTol = 1.0e-7
# cast to arrays (in case they aren't)
if num.isscalar(eta0):
eta0 = [eta0]
if num.isscalar(tth0):
tth0 = [tth0]
if num.isscalar(ome0):
ome0 = [ome0]
eta0 = num.asarray(eta0)
tth0 = num.asarray(tth0)
ome0 = num.asarray(ome0)
if eta0.ndim != 1:
raise RuntimeError, "your azimuthal input was not 1-D, so I do not know what you expect me to do"
npts = len(eta0)
if tth0.ndim != 1:
raise RuntimeError, "your Bragg angle input was not 1-D, so I do not know what you expect me to do"
else:
if len(tth0) != npts:
if len(tth0) == 1:
tth0 = tth0 * num.ones(npts)
elif npts == 1:
npts = len(tth0)
eta0 = eta0 * num.ones(npts)
else:
raise RuntimeError, "the azimuthal and Bragg angle inputs are inconsistent"
if len(ome0) == 0:
ome0 = num.zeros(npts) # dummy ome0
elif len(ome0) == 1 and npts > 1:
ome0 = ome0 * num.ones(npts)
else:
if len(ome0) != npts:
raise RuntimeError(
"your oscialltion angle input is inconsistent; "
+ "it has length %d while it should be %d" % (len(ome0), npts)
)
# keyword args processing
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == "display":
dispFlag = kwargs[argkeys[i]]
elif argkeys[i] == "convention":
if kwargs[argkeys[i]].lower() == "fable":
fableFlag = True
elif argkeys[i] == "units":
if kwargs[argkeys[i]] == "radians":
c1 = 180.0 / pi
c2 = 1.0
elif argkeys[i] == "chiTilt":
if kwargs[argkeys[i]] is not None:
chi = kwargs[argkeys[i]]
# a little talkback...
if dispFlag:
if fableFlag:
print "\nUsing Fable angle convention\n"
else:
print "\nUsing image-based angle convention\n"
# mapped eta input
# - in DEGREES, thanks to c1
eta0 = mapAngle(c1 * eta0, [-180, 180], units="degrees")
if fableFlag:
eta0 = 90 - eta0
# must put args into RADIANS
# - eta0 is in DEGREES,
# - the others are in whatever was entered, hence c2
eta0 = d2r * eta0
tht0 = c2 * tth0 / 2
if chi is not None:
chi = c2 * chi
else:
chi = 0
# ---------------------
# SYSTEM SOLVE
#
#
# cos(chi)cos(eta)cos(theta)sin(x) - cos(chi)sin(theta)cos(x) = sin(theta) - sin(chi)sin(eta)cos(theta)
#
#
# Identity: a sin x + b cos x = sqrt(a**2 + b**2) sin (x + alfa)
#
# /
# | atan(b/a) for a > 0
# alfa <
# | pi + atan(b/a) for a < 0
# \
#
# => sin (x + alfa) = c / sqrt(a**2 + b**2)
#
# must use both branches for sin(x) = n: x = u (+ 2k*pi) | x = pi - u (+ 2k*pi)
#
cchi = num.cos(chi)
schi = num.sin(chi)
ceta = num.cos(eta0)
seta = num.sin(eta0)
ctht = num.cos(tht0)
stht = num.sin(tht0)
nchi = num.c_[0.0, cchi, schi].T
gHat0_l = -num.vstack([ceta * ctht, seta * ctht, stht])
a = cchi * ceta * ctht
b = -cchi * stht
c = stht + schi * seta * ctht
# form solution
abMag = num.sqrt(a * a + b * b)
assert num.all(abMag > 0), "Beam vector specification is infeasible!"
phaseAng = num.arctan2(b, a)
rhs = c / abMag
rhs[abs(rhs) > 1.0] = num.nan
rhsAng = num.arcsin(rhs)
# write ome angle output arrays (NaNs persist here)
ome1 = rhsAng - phaseAng
ome2 = num.pi - rhsAng - phaseAng
ome1 = mapAngle(ome1, [-num.pi, num.pi], units="radians")
ome2 = mapAngle(ome2, [-num.pi, num.pi], units="radians")
ome_stack = num.vstack([ome1, ome2])
min_idx = num.argmin(abs(ome_stack), axis=0)
ome_min = ome_stack[min_idx, range(len(ome1))]
eta_min = num.nan * num.ones_like(ome_min)
# mark feasible reflections
goodOnes = -num.isnan(ome_min)
numGood = sum(goodOnes)
tmp_eta = num.empty(numGood)
tmp_gvec = gHat0_l[:, goodOnes]
for i in range(numGood):
come = num.cos(ome_min[goodOnes][i])
some = num.sin(ome_min[goodOnes][i])
rchi = rotMatOfExpMap(num.tile(ome_min[goodOnes][i], (3, 1)) * nchi)
gHat_l = num.dot(rchi, tmp_gvec[:, i].reshape(3, 1))
tmp_eta[i] = num.arctan2(gHat_l[1], gHat_l[0])
pass
eta_min[goodOnes] = tmp_eta
# everybody back to DEGREES!
# - ome1 is in RADIANS here
# - convert and put into [-180, 180]
ome1 = mapAngle(mapAngle(r2d * ome_min, [-180, 180], units="degrees") + c1 * ome0, [-180, 180], units="degrees")
# put eta1 in [-180, 180]
eta1 = mapAngle(r2d * eta_min, [-180, 180], units="degrees")
if not outputDegrees:
ome1 = d2r * ome1
eta1 = d2r * eta1
return ome1, eta1
def latticeVectors(lparms, tag='cubic', radians=False, debug=False):
"""
Generates direct and reciprocal lattice vector components in a
crystal-relative RHON basis, X. The convention for fixing X to the
lattice is such that a || x1 and c* || x3, where a and c* are
direct and reciprocal lattice vectors, respectively.
USAGE:
lattice = LatticeVectors(lparms, <symmTag>)
INPUTS:
1) lparms (1 x n float list) is the array of lattice parameters,
where n depends on the symmetry group (see below).
2) symTag (string) is a case-insensitive string representing the
symmetry type of the implied Laue group. The 11 available choices
are shown below. The default value is 'cubic'. Note that each
group expects a lattice parameter array of the indicated length
and order.
latticeType lparms
----------- ------------
'cubic' a
'hexagonal' a, c
'trigonal' a, c
'rhombohedral' a, alpha (in degrees)
'tetragonal' a, c
'orthorhombic' a, b, c
'monoclinic' a, b, c, beta (in degrees)
'triclinic' a, b, c, alpha, beta, gamma (in degrees)
OUTPUTS:
1) lattice is a dictionary containing the following keys/items:
F (3, 3) double array transformation matrix taking
componenents in the direct
lattice (i.e. {uvw}) to the
reference, X
B (3, 3) double array transformation matrix taking
componenents in the reciprocal
lattice (i.e. {hkl}) to X
BR (3, 3) double array transformation matrix taking
componenents in the reciprocal
lattice to the Fable reference
frame (see notes)
U0 (3, 3) double array transformation matrix
(orthogonal) taking
componenents in the
Fable reference frame to X
vol double the unit cell volume
dparms (6, ) double list the direct lattice parameters:
[a b c alpha beta gamma]
rparms (6, ) double list the reciprocal lattice
parameters:
[a* b* c* alpha* beta* gamma*]
NOTES:
*) The conventions used for assigning a RHON basis,
X -> {x1, x2, x3}, to each point group are consistent with
those published in Appendix B of [1]. Namely: a || x1 and
c* || x3. This differs from the convention chosen by the Fable
group, where a* || x1 and c || x3 [2].
*) The unit cell angles are defined as follows:
alpha=acos(b'*c/|b||c|), beta=acos(c'*a/|c||a|), and
gamma=acos(a'*b/|a||b|).
*) The reciprocal lattice vectors are calculated using the
crystallographic convention, where the prefactor of 2*pi is
omitted. In this convention, the reciprocal lattice volume is
1/V.
*) Several relations from [3] were employed in the component
calculations.
REFERENCES:
[1] J. F. Nye, ``Physical Properties of Crystals: Their
Representation by Tensors and Matrices''. Oxford University
Press, 1985. ISBN 0198511655
[2] E. M. Lauridsen, S. Schmidt, R. M. Suter, and H. F. Poulsen,
``Tracking: a method for structural characterization of grains
in powders or polycrystals''. J. Appl. Cryst. (2001). 34,
744--750
[3] R. J. Neustadt, F. W. Cagle, Jr., and J. Waser, ``Vector
algebra and the relations between direct and reciprocal
lattice quantities''. Acta Cryst. (1968), A24, 247--248
"""
# build index for sorting out lattice parameters
lattStrings = [
'cubic' ,
'hexagonal' ,
'trigonal' ,
'rhombohedral',
'tetragonal' ,
'orthorhombic',
'monoclinic' ,
'triclinic'
]
if radians:
angConv = 1.
else:
angConv = pi/180. # degToRad
deg90 = pi/2.
deg120 = 2.*pi/3.
#
if tag == lattStrings[0]: # cubic
cellparms = num.r_[num.tile(lparms[0], (3,)), deg90*num.ones((3,))]
elif tag == lattStrings[1] or tag == lattStrings[2]: # hexagonal | trigonal (hex indices)
cellparms = num.r_[lparms[0], lparms[0], lparms[1], deg90, deg90, deg120]
elif tag == lattStrings[3]: # rhombohedral
cellparms = num.r_[num.tile(lparms[0], (3,)), num.tile(angConv*lparms[1], (3,))]
elif tag == lattStrings[4]: # tetragonal
cellparms = num.r_[lparms[0], lparms[0], lparms[1], deg90, deg90, deg90]
elif tag == lattStrings[5]: # orthorhombic
cellparms = num.r_[lparms[0], lparms[1], lparms[2], deg90, deg90, deg90]
elif tag == lattStrings[6]: # monoclinic
cellparms = num.r_[lparms[0], lparms[1], lparms[2], deg90, angConv*lparms[3], deg90]
elif tag == lattStrings[7]: # triclinic
cellparms = lparms
else:
raise RuntimeError('lattice tag \'%s\' is not recognized' % (tag))
if debug:
print str(cellparms[0:3]) + ' ' + str(r2d*cellparms[3:6])
alfa = cellparms[3]
beta = cellparms[4]
gama = cellparms[5]
cosalfar, sinalfar = cosineXform(alfa, beta, gama)
a = cellparms[0]*num.r_[1, 0, 0]
b = cellparms[1]*num.r_[num.cos(gama), num.sin(gama), 0]
c = cellparms[2]*num.r_[num.cos(beta), -cosalfar*num.sin(beta), sinalfar*num.sin(beta)]
ad = num.sqrt(sum(a**2))
bd = num.sqrt(sum(b**2))
cd = num.sqrt(sum(c**2))
# Cell volume
V = num.dot(a, num.cross(b, c))
# F takes components in the direct lattice to X
F = num.c_[a, b, c]
# Reciprocal lattice vectors
astar = num.cross(b, c)/V
bstar = num.cross(c, a)/V
cstar = num.cross(a, b)/V
# and parameters
ar = num.sqrt(sum(astar**2))
br = num.sqrt(sum(bstar**2))
cr = num.sqrt(sum(cstar**2))
alfar = num.arccos(num.dot(bstar, cstar)/br/cr)
betar = num.arccos(num.dot(cstar, astar)/cr/ar)
gamar = num.arccos(num.dot(astar, bstar)/ar/br)
# B takes components in the reciprocal lattice to X
B = num.c_[astar, bstar, cstar]
cosalfar2, sinalfar2 = cosineXform(alfar, betar, gamar)
afable = ar*num.r_[1, 0, 0]
bfable = br*num.r_[num.cos(gamar), num.sin(gamar), 0]
cfable = cr*num.r_[num.cos(betar), -cosalfar2*num.sin(betar), sinalfar2*num.sin(betar)]
BR = num.c_[afable, bfable, cfable]
U0 = num.dot(B, num.linalg.inv(BR))
if outputDegrees:
dparms = num.r_[ad, bd, cd, r2d*num.r_[ alfa, beta, gama]]
rparms = num.r_[ar, br, cr, r2d*num.r_[alfar, betar, gamar]]
else:
dparms = num.r_[ad, bd, cd, num.r_[ alfa, beta, gama]]
rparms = num.r_[ar, br, cr, num.r_[alfar, betar, gamar]]
L = {'F':F,
'B':B,
'BR':BR,
'U0':U0,
'vol':V,
'dparms':dparms,
'rparms':rparms}
return L
def makeScatteringVectors(hkls, rMat_c, bMat, wavelength, chiTilt=None):
"""
modeled after QFromU.m
"""
# basis vectors
bHat_l = num.c_[ 0., 0., -1.].T
eHat_l = num.c_[ 1., 0., 0.].T
zTol = 1.0e-7 # zero tolerance for checking vectors
gVec_s = []
oangs0 = []
oangs1 = []
# these are the reciprocal lattice vectors in the CRYSTAL FRAME
# ** NOTE **
# if strained, assumes that you handed it a bMat calculated from
# strained [a, b, c]
gVec_c = num.dot( bMat, hkls )
gHat_c = unitVector(gVec_c)
dim0, nRefl = gVec_c.shape
assert dim0 == 3, "Looks like something is wrong with your lattice plane normals son!"
# extract 1/dspacing and sin of bragg angle
dSpacingi = columnNorm(gVec_c).flatten()
sintht = 0.5 * wavelength * dSpacingi
# move reciprocal lattice vectors to sample frame
gHat_s = num.dot(rMat_c.squeeze(), gHat_c)
if chiTilt is None:
cchi = 1.
schi = 0.
rchi = num.eye(3)
else:
cchi = num.cos(chiTilt)
schi = num.sin(chiTilt)
rchi = num.array([[ 1., 0., 0.],
[ 0., cchi, -schi],
[ 0., schi, cchi]])
pass
a = cchi * gHat_s[0, :]
b = -cchi * gHat_s[2, :]
c = schi * gHat_s[1, :] - sintht
# form solution
abMag = num.sqrt(a*a + b*b); assert num.all(abMag > 0), "Beam vector specification is infealible!"
phaseAng = num.arctan2(b, a)
rhs = c / abMag; rhs[abs(rhs) > 1.] = num.nan
rhsAng = num.arcsin(rhs)
# write ome angle output arrays (NaNs persist here)
ome0 = rhsAng - phaseAng
ome1 = num.pi - rhsAng - phaseAng
goodOnes_s = -num.isnan(ome0)
eta0 = num.nan * num.ones_like(ome0)
eta1 = num.nan * num.ones_like(ome1)
# mark feasible reflections
goodOnes = num.tile(goodOnes_s, (1, 2)).flatten()
numGood_s = sum(goodOnes_s)
numGood = 2 * numGood_s
tmp_eta = num.empty(numGood)
tmp_gvec = num.tile(gHat_c, (1, 2))[:, goodOnes]
allome = num.hstack([ome0, ome1])
for i in range(numGood):
come = num.cos(allome[goodOnes][i])
some = num.sin(allome[goodOnes][i])
rome = num.array([[ come, 0., some],
[ 0., 1., 0.],
[-some, 0., come]])
rMat_s = num.dot(rchi, rome)
gVec_l = num.dot(rMat_s,
num.dot(rMat_c, tmp_gvec[:, i].reshape(3, 1)
) )
tmp_eta[i] = num.arctan2(gVec_l[1], gVec_l[0])
pass
eta0[goodOnes_s] = tmp_eta[:numGood_s]
eta1[goodOnes_s] = tmp_eta[numGood_s:]
# make assoc tTh array
tTh = 2.*num.arcsin(sintht).flatten()
tTh0 = tTh; tTh0[-goodOnes_s] = num.nan
gVec_s = num.tile(dSpacingi, (3, 1)) * gHat_s
oangs0 = num.vstack([tTh0.flatten(), eta0.flatten(), ome0.flatten()])
oangs1 = num.vstack([tTh0.flatten(), eta1.flatten(), ome1.flatten()])
return gVec_s, oangs0, oangs1
def getFriedelPair(tth0, eta0, *ome0, **kwargs):
"""
Get the diffractometer angular coordinates in degrees for
the Friedel pair of a given reflection (min angular distance).
AUTHORS:
J. V. Bernier -- 10 Nov 2009
USAGE:
ome1, eta1 = getFriedelPair(tth0, eta0, *ome0,
display=False,
units='degrees',
convention='hexrd')
INPUTS:
1) tth0 is a list (or ndarray) of 1 or n the bragg angles (2theta) for
the n reflections (tiled to match eta0 if only 1 is given).
2) eta0 is a list (or ndarray) of 1 or n azimuthal coordinates for the n
reflections (tiled to match tth0 if only 1 is given).
3) ome0 is a list (or ndarray) of 1 or n reference oscillation
angles for the n reflections (denoted omega in [1]). This argument
is optional.
4) Keyword arguments may be one of the following:
Keyword Values|{default} Action
-------------- -------------- --------------
'display' True|{False} toggles display info to cmd line
'units' 'radians'|{'degrees'} sets units for input angles
'convention' 'fable'|{'hexrd'} sets conventions defining
the angles (see below)
'chiTilt' None the inclination (about Xlab) of
the oscillation axis
OUTPUTS:
1) ome1 contains the oscialltion angle coordinates of the
Friedel pairs associated with the n input reflections, relative to ome0
(i.e. ome1 = <result> + ome0). Output is in DEGREES!
2) eta1 contains the azimuthal coordinates of the Friedel
pairs associated with the n input reflections. Output units are
controlled via the module variable 'outputDegrees'
NOTES:
JVB) The ouputs ome1, eta1 are written using the selected convention, but the
units are alway degrees. May change this to work with Nathan's global...
JVB) In the 'fable' convention [1], {XYZ} form a RHON basis where X is
downstream, Z is vertical, and eta is CCW with +Z defining eta = 0.
JVB) In the 'hexrd' convention [2], {XYZ} form a RHON basis where Z is upstream,
Y is vertical, and eta is CCW with +X defining eta = 0.
REFERENCES:
[1] E. M. Lauridsen, S. Schmidt, R. M. Suter, and H. F. Poulsen,
``Tracking: a method for structural characterization of grains in
powders or polycrystals''. J. Appl. Cryst. (2001). 34, 744--750
[2] J. V. Bernier, M. P. Miller, J. -S. Park, and U. Lienert,
``Quantitative Stress Analysis of Recrystallized OFHC Cu Subject
to Deformed In Situ'', J. Eng. Mater. Technol. (2008). 130.
DOI:10.1115/1.2870234
"""
dispFlag = False
fableFlag = False
chi = None
c1 = 1.
c2 = pi/180.
zTol = 1.e-7
# cast to arrays (in case they aren't)
if num.isscalar(eta0):
eta0 = [eta0]
if num.isscalar(tth0):
tth0 = [tth0]
if num.isscalar(ome0):
ome0 = [ome0]
eta0 = num.asarray(eta0)
tth0 = num.asarray(tth0)
ome0 = num.asarray(ome0)
if eta0.ndim != 1:
raise RuntimeError, 'your azimuthal input was not 1-D, so I do not know what you expect me to do'
npts = len(eta0)
if tth0.ndim != 1:
raise RuntimeError, 'your Bragg angle input was not 1-D, so I do not know what you expect me to do'
else:
if len(tth0) != npts:
if len(tth0) == 1:
tth0 = tth0*num.ones(npts)
elif npts == 1:
npts = len(tth0)
eta0 = eta0*num.ones(npts)
else:
raise RuntimeError, 'the azimuthal and Bragg angle inputs are inconsistent'
if len(ome0) == 0:
ome0 = num.zeros(npts) # dummy ome0
elif len(ome0) == 1 and npts > 1:
ome0 = ome0*num.ones(npts)
else:
if len(ome0) != npts:
raise RuntimeError('your oscialltion angle input is inconsistent; ' \
+ 'it has length %d while it should be %d' % (len(ome0), npts) )
# keyword args processing
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'display':
dispFlag = kwargs[argkeys[i]]
elif argkeys[i] == 'convention':
if kwargs[argkeys[i]].lower() == 'fable':
fableFlag = True
elif argkeys[i] == 'units':
if kwargs[argkeys[i]] == 'radians':
c1 = 180./pi
c2 = 1.
elif argkeys[i] == 'chiTilt':
if kwargs[argkeys[i]] is not None:
chi = kwargs[argkeys[i]]
# a little talkback...
if dispFlag:
if fableFlag:
print '\nUsing Fable angle convention\n'
else:
print '\nUsing image-based angle convention\n'
# mapped eta input
# - in DEGREES, thanks to c1
eta0 = mapAngle(c1*eta0, [-180, 180], units='degrees')
if fableFlag:
eta0 = 90 - eta0
# must put args into RADIANS
# - eta0 is in DEGREES,
# - the others are in whatever was entered, hence c2
eta0 = d2r*eta0
tht0 = c2*tth0/2
if chi is not None:
chi = c2*chi
else:
chi = 0
# ---------------------
# SYSTEM SOLVE
#
#
# cos(chi)cos(eta)cos(theta)sin(x) - cos(chi)sin(theta)cos(x) = sin(theta) - sin(chi)sin(eta)cos(theta)
#
#
# Identity: a sin x + b cos x = sqrt(a**2 + b**2) sin (x + alfa)
#
# /
# | atan(b/a) for a > 0
# alfa <
# | pi + atan(b/a) for a < 0
# \
#
# => sin (x + alfa) = c / sqrt(a**2 + b**2)
#
# must use both branches for sin(x) = n: x = u (+ 2k*pi) | x = pi - u (+ 2k*pi)
#
cchi = num.cos(chi); schi = num.sin(chi)
ceta = num.cos(eta0); seta = num.sin(eta0)
ctht = num.cos(tht0); stht = num.sin(tht0)
nchi = num.c_[0., cchi, schi].T
gHat0_l = num.vstack([ceta * ctht,
seta * ctht,
stht])
a = cchi*ceta*ctht
b = cchi*schi*seta*ctht + schi*schi*stht - stht
c = stht + cchi*schi*seta*ctht + schi*schi*stht
# form solution
abMag = num.sqrt(a*a + b*b); assert num.all(abMag > 0), "Beam vector specification is infealible!"
phaseAng = num.arctan2(b, a)
rhs = c / abMag; rhs[abs(rhs) > 1.] = num.nan
rhsAng = num.arcsin(rhs)
# write ome angle output arrays (NaNs persist here)
ome1 = rhsAng - phaseAng
ome2 = num.pi - rhsAng - phaseAng
ome1 = mapAngle(ome1, [-num.pi, num.pi], units='radians')
ome2 = mapAngle(ome2, [-num.pi, num.pi], units='radians')
ome_stack = num.vstack([ome1, ome2])
min_idx = num.argmin(abs(ome_stack), axis=0)
ome_min = ome_stack[min_idx, range(len(ome1))]
eta_min = num.nan * num.ones_like(ome_min)
# mark feasible reflections
goodOnes = -num.isnan(ome_min)
numGood = sum(goodOnes)
tmp_eta = num.empty(numGood)
tmp_gvec = gHat0_l[:, goodOnes]
for i in range(numGood):
come = num.cos(ome_min[goodOnes][i])
some = num.sin(ome_min[goodOnes][i])
rchi = rotMatOfExpMap( num.tile(ome_min[goodOnes][i], (3, 1)) * nchi )
gHat_l = num.dot(rchi, tmp_gvec[:, i].reshape(3, 1))
tmp_eta[i] = num.arctan2(gHat_l[1], gHat_l[0])
pass
eta_min[goodOnes] = tmp_eta
# everybody back to DEGREES!
# - ome1 is in RADIANS here
# - convert and put into [-180, 180]
ome1 = mapAngle( mapAngle(r2d*ome_min, [-180, 180], units='degrees') + c1*ome0, [-180, 180], units='degrees')
# put eta1 in [-180, 180]
eta1 = mapAngle(r2d*eta_min, [-180, 180], units='degrees')
if not outputDegrees:
ome1 = d2r * ome1
eta1 = d2r * eta1
return ome1, eta1