def writeGVE(spotsArray, fileroot, **kwargs):
"""
write Fable gve file from Spots object
fileroot is the root string used to write the gve and ini files
Outputs:
No return value, but writes the following files:
<fileroot>.gve
<fileroot>_grainSpotter.ini (points to --> <fileroot>_grainSpotter.log)
Keyword arguments:
Mainly for GrainSpotter .ini file, but some are needed for gve files
keyword default definitions
-----------------------------------------------------------------------------------------
'sgNum': <225>
'phaseID': <None>
'cellString': <F>
'omeRange': <-60, 60, 120, 240> the oscillation range(s) **currently pulls from spots
'deltaOme': <0.25, 0.25> the oscillation delta(s) **currently pulls from spots
'minMeas': <24>
'minCompl': <0.7>
'minUniqn': <0.5>
'uncertainty': <[0.10, 0.25, .50]> the min [tTh, eta, ome] uncertainties in degrees
'eulStep': <2>
'nSigmas': <2>
'minFracG': <0.90>
'nTrials': <100000>
'positionfit': <True>
Notes:
*) The omeRange is currently pulled from the spotsArray input; the kwarg has no effect
as of now. Will change this to 'override' the spots info if the user, say, wants to
pare down the range.
*) There is no etaRange argument yet, but presumably GrainSpotter knows how to deal
with this. Pending feature...
"""
# check on fileroot
assert isinstance(fileroot, str)
# keyword argument processing
phaseID = None
sgNum = 225
cellString = 'P'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = True
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (argkeys[i])
# grab some detector geometry parameters for gve file header
mmPerPixel = float(spotsArray.detectorGeom.pixelPitch) # ...these are still hard-coded to be square
nrows_p = spotsArray.detectorGeom.nrows - 1
ncols_p = spotsArray.detectorGeom.ncols - 1
row_p, col_p = spotsArray.detectorGeom.pixelIndicesOfCartesianCoords(spotsArray.detectorGeom.xc,
spotsArray.detectorGeom.yc)
yc_p = ncols_p - col_p
zc_p = nrows_p - row_p
wd_mu = spotsArray.detectorGeom.workDist * 1e3 # in microns (Soeren)
osc_axis = num.dot(fableSampCOB.T, Yl).flatten()
# start grabbing stuff from planeData
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d*tThRng.min(), r2d*tThRng.max()) # single range should be ok since entering hkls
etaMin, etaMax = (0, 360) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
if hasattr(omeMin[iOme], 'getVal'):
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme].getVal('degrees'), omeMax[iOme].getVal('degrees'))
else:
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d, omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d*cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (1/dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sR, sC, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5*sTTh) # dspacing
# get raw y, z (Fable frame)
yraw = ncols_p - sC
zraw = nrows_p - sR
# convert eta to fable frame
rEta = mapAngle(90. - r2d*sEta, [0, 360], units='degrees')
# make mesaured G vector components in fable frame
mGvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='fable', frame='sample')
# full Gvec components in fable lab frame (for grainspotter position fit)
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh, sEta, sOme, outputGve=True)
# no 4*pi
mGvec = mGvec / sDsp
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sR, sC, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
pass
# write gve file for grainspotter
fid = open(fileroot+'.gve', 'w')
print >> fid, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n' + \
'# axis = %d %d %d\n' % tuple(osc_axis) + \
'# cell__a %1.4f\n' %(cellp[0]) + \
'# cell__b %1.4f\n' %(cellp[1]) + \
'# cell__c %1.4f\n' %(cellp[2]) + \
'# cell_alpha %1.4f\n' %(cellp[3]) + \
'# cell_beta %1.4f\n' %(cellp[4]) + \
'# cell_gamma %1.4f\n' %(cellp[5]) + \
'# cell_lattice_[P,A,B,C,I,F,R] %s\n' %(cellString) + \
'# chi 0.0\n' + \
'# distance %.4f\n' %(wd_mu) + \
'# fit_tolerance 0.5\n' + \
'# o11 1\n' + \
'# o12 0\n' + \
'# o21 0\n' + \
'# o22 -1\n' + \
'# omegasign %1.1f\n' %(num.sign(deltaOme)) + \
'# t_x 0\n' + \
'# t_y 0\n' + \
'# t_z 0\n' + \
'# tilt_x 0.000000\n' + \
'# tilt_y 0.000000\n' + \
'# tilt_z 0.000000\n' + \
'# y_center %.6f\n' %(yc_p) + \
'# y_size %.6f\n' %(mmPerPixel*1.e3) + \
'# z_center %.6f\n' %(zc_p) + \
'# z_size %.6f\n' %(mmPerPixel*1.e3) + \
'# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
fid.close()
###############################################################
# GrainSpotter ini parameters
#
# fileroot = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
fid = open(fileroot+'_grainSpotter.ini', 'w')
# self.__tempFNameList.append(fileroot)
print >> fid, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s_grainSpotter.log\n' % (fileroot, fileroot) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
fid.close()
return
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
set12 = eta0 > 90.0
lw = 2
fig1 = plt.figure(1)
fig1.clf()
axes1 = fig1.gca()
fig2 = plt.figure(2)
fig2.clf()
axes2 = fig2.gca()
for i in range(len(chi)):
ome1, eta1 = xtl.getFriedelPair(tth0, eta0, chiTilt=chi[i], units="degrees", convention="hexrd")
axes1.plot(d2r * eta0[set11], ome1[set11], lt[i], label="$\chi$=%d$^\circ$" % chi[i], linewidth=lw)
axes1.plot(d2r * eta0[set12], ome1[set12], lt[i], label="$\chi$=%d$^\circ$" % chi[i], linewidth=lw)
# eta = np.pi - rot.angularDifference(d2r*eta0, eta1)
eta = rot.mapAngle(np.pi - (d2r * eta0 - eta1))
set1 = np.logical_and(eta0 <= 0.0, eta >= 0.0)
set2 = np.logical_and(eta0 <= 0.0, eta <= 0.0)
set3 = eta0 >= 0.0
axes2.plot(d2r * eta0, eta, lt[i], linewidth=lw)
# axes2.plot(d2r*eta0[set1], eta[set1], lt[i], linewidth=lw)
# axes2.plot(d2r*eta0[set2], eta[set2], lt[i], linewidth=lw)
# axes2.plot(d2r*eta0[set3], eta[set3], lt[i], linewidth=lw)
axes1.grid(True)
axes1.axis("tight")
axes1.set_xlabel("starting azimuth, $\eta_0$")
axes1.set_ylabel("minimum $\Delta\omega_{FP}$")
def writeGVE(spotsArray, fileroot, **kwargs):
"""
write Fable gve file from Spots object
fileroot is the root string used to write the gve and ini files
Outputs:
No return value, but writes the following files:
<fileroot>.gve
<fileroot>_grainSpotter.ini (points to --> <fileroot>_grainSpotter.log)
Keyword arguments:
Mainly for GrainSpotter .ini file, but some are needed for gve files
keyword default definitions
-----------------------------------------------------------------------------------------
'sgNum': <225>
'phaseID': <None>
'cellString': <F>
'omeRange': <-60, 60, 120, 240> the oscillation range(s) **currently pulls from spots
'deltaOme': <0.25, 0.25> the oscillation delta(s) **currently pulls from spots
'minMeas': <24>
'minCompl': <0.7>
'minUniqn': <0.5>
'uncertainty': <[0.10, 0.25, .50]> the min [tTh, eta, ome] uncertainties in degrees
'eulStep': <2>
'nSigmas': <2>
'minFracG': <0.90>
'nTrials': <100000>
'positionfit': <True>
Notes:
*) The omeRange is currently pulled from the spotsArray input; the kwarg has no effect
as of now. Will change this to 'override' the spots info if the user, say, wants to
pare down the range.
*) There is no etaRange argument yet, but presumably GrainSpotter knows how to deal
with this. Pending feature...
"""
# check on fileroot
assert isinstance(fileroot, str)
# keyword argument processing
phaseID = None
sgNum = 225
cellString = 'P'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = True
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (
argkeys[i])
# grab some detector geometry parameters for gve file header
mmPerPixel = float(spotsArray.detectorGeom.pixelPitch
) # ...these are still hard-coded to be square
nrows_p = spotsArray.detectorGeom.nrows - 1
ncols_p = spotsArray.detectorGeom.ncols - 1
row_p, col_p = spotsArray.detectorGeom.pixelIndicesOfCartesianCoords(
spotsArray.detectorGeom.xc, spotsArray.detectorGeom.yc)
yc_p = ncols_p - col_p
zc_p = nrows_p - row_p
wd_mu = spotsArray.detectorGeom.workDist * 1e3 # in microns (Soeren)
osc_axis = num.dot(fableSampCOB.T, Yl).flatten()
# start grabbing stuff from planeData
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d * tThRng.min(), r2d * tThRng.max()
) # single range should be ok since entering hkls
etaMin, etaMax = (
0, 360
) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
if hasattr(omeMin[iOme], 'getVal'):
omeRangeString += 'omegarange %g %g\n' % (
omeMin[iOme].getVal('degrees'), omeMax[iOme].getVal('degrees'))
else:
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d,
omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d * cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (
1 / dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sR, sC, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5 * sTTh) # dspacing
# get raw y, z (Fable frame)
yraw = ncols_p - sC
zraw = nrows_p - sR
# convert eta to fable frame
rEta = mapAngle(90. - r2d * sEta, [0, 360], units='degrees')
# make mesaured G vector components in fable frame
mGvec = makeMeasuredScatteringVectors(sTTh,
sEta,
sOme,
convention='fable',
frame='sample')
# full Gvec components in fable lab frame (for grainspotter position fit)
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh,
sEta,
sOme,
outputGve=True)
# no 4*pi
mGvec = mGvec / sDsp
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sR, sC, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
pass
# write gve file for grainspotter
fid = open(fileroot + '.gve', 'w')
print >> fid, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n' + \
'# axis = %d %d %d\n' % tuple(osc_axis) + \
'# cell__a %1.4f\n' %(cellp[0]) + \
'# cell__b %1.4f\n' %(cellp[1]) + \
'# cell__c %1.4f\n' %(cellp[2]) + \
'# cell_alpha %1.4f\n' %(cellp[3]) + \
'# cell_beta %1.4f\n' %(cellp[4]) + \
'# cell_gamma %1.4f\n' %(cellp[5]) + \
'# cell_lattice_[P,A,B,C,I,F,R] %s\n' %(cellString) + \
'# chi 0.0\n' + \
'# distance %.4f\n' %(wd_mu) + \
'# fit_tolerance 0.5\n' + \
'# o11 1\n' + \
'# o12 0\n' + \
'# o21 0\n' + \
'# o22 -1\n' + \
'# omegasign %1.1f\n' %(num.sign(deltaOme)) + \
'# t_x 0\n' + \
'# t_y 0\n' + \
'# t_z 0\n' + \
'# tilt_x 0.000000\n' + \
'# tilt_y 0.000000\n' + \
'# tilt_z 0.000000\n' + \
'# y_center %.6f\n' %(yc_p) + \
'# y_size %.6f\n' %(mmPerPixel*1.e3) + \
'# z_center %.6f\n' %(zc_p) + \
'# z_size %.6f\n' %(mmPerPixel*1.e3) + \
'# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
fid.close()
###############################################################
# GrainSpotter ini parameters
#
# fileroot = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
fid = open(fileroot + '_grainSpotter.ini', 'w')
# self.__tempFNameList.append(fileroot)
print >> fid, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s_grainSpotter.log\n' % (fileroot, fileroot) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
fid.close()
return
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
def __call__(self, spotsArray, **kwargs):
"""
A word on spacegroup numbers: it appears that grainspotter is using the 'VolA' tag for calls to SgInfo
"""
location = self.__class__.__name__
tic = time.time()
# keyword argument processing
phaseID = None
gVecFName = 'tmpGve'
sgNum = 225
cellString = 'F'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = False
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'gVecFName':
gVecFName = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (argkeys[i])
# cleanup stuff from any previous run
self.cleanup()
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d*tThRng.min(), r2d*tThRng.max()) # single range should be ok since entering hkls
etaMin, etaMax = (0, 360) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d, omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d*cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (1/dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
ii = 0
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sX, sY, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5*sTTh) # dspacing
# convert eta to risoe frame
rEta = mapAngle(90. - r2d*sEta, [0, 360], units='degrees')
# make mesaured G vector components in risoe frame
mGvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='risoe', frame='sample')
# mQvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='llnl', frame='lab')
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh, sEta, sOme, outputGve=True)
mGvec = mGvec / sDsp
# mQvec = 4*num.pi*num.sin(0.5*sTTh)*mQvec/wlen
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sX, sY, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
# advance counter
ii += 1
# write gve file for grainspotter
f = open(gVecFName+'.gve', 'w')
print >> f, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
f.close()
###############################################################
# GrainSpotter ini parameters
#
# tempFNameIn = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
tempFNameIn = 'tmpIni'
f = open(tempFNameIn, 'w')
# self.__tempFNameList.append(tempFNameIn)
print >> f, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s.log\n' % (gVecFName, tempFNameIn) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
f.close()
toc = time.time()
print 'in %s, setup took %g' % (location, toc-tic)
tic = time.time()
# tempFNameStdout = tempfile.mktemp()
# self.__tempFNameList.append(tempFNameStdout)
tempFNameStdout = 'tmp.out'
# grainSpotterCmd = '%s %s > %s' % (self.__execName, tempFNameIn, tempFNameStdout)
grainSpotterCmd = '%s %s' % (self.__execName, tempFNameIn)
os.system(grainSpotterCmd)
toc = time.time()
print 'in %s, execution took %g' % (location, toc-tic)
tic = time.time()
# add output files to cleanup list
# self.__tempFNameList += glob.glob(tempFNameIn+'.*')
# collect data from gff file'
gffFile = tempFNameIn+'.gff'
gffData = num.loadtxt(gffFile)
if gffData.ndim == 1:
gffData = gffData.reshape(1, len(gffData))
gffData_U = gffData[:,6:6+9]
# process for output
retval = convertUToRotMat(gffData_U, U0, symTag=symTag)
toc = time.time()
print 'in %s, post-processing took %g' % (location, toc-tic)
tic = time.time()
return retval
