def get_job_queue(cfg):
job_queue = mp.JoinableQueue()
# load the queue
try:
estimate_f = cfg.fit_grains.estimate
grain_params_list = np.loadtxt(estimate_f)
n_quats = len(grain_params_list)
for grain_params in grain_params_list:
grain_id = grain_params[0]
job_queue.put((grain_id, grain_params[3:15]))
logger.info(
'fitting grains using "%s" for the initial estimate',
estimate_f
)
except (ValueError, IOError):
logger.info('fitting grains using default initial estimate')
# load quaternion file
quats = np.atleast_2d(
np.loadtxt(os.path.join(cfg.analysis_dir, 'quats.out'))
)
n_quats = len(quats)
quats = quats.T
phi, n = angleAxisOfRotMat(rotMatOfQuat(quats))
for i, quat in enumerate(quats.T):
exp_map = phi[i]*n[:, i]
grain_params = np.hstack(
[exp_map.flatten(), 0., 0., 0., 1., 1., 1., 0., 0., 0.]
)
job_queue.put((i, grain_params))
logger.info("fitting grains for %d orientations", n_quats)
return job_queue
def get_job_queue(cfg, ids_to_refine=None):
job_queue = mp.JoinableQueue()
# load the queue
try:
# use an estimate of the grain parameters, if available
estimate_f = cfg.fit_grains.estimate
grain_params_list = np.atleast_2d(np.loadtxt(estimate_f))
n_quats = len(grain_params_list)
n_jobs = 0
for grain_params in grain_params_list:
grain_id = grain_params[0]
if ids_to_refine is None or grain_id in ids_to_refine:
job_queue.put((grain_id, grain_params[3:15]))
n_jobs += 1
logger.info('fitting grains using "%s" for the initial estimate',
estimate_f)
except (ValueError, IOError):
# no estimate available, use orientations and defaults
logger.info('fitting grains using default initial estimate')
# load quaternion file
quats = np.atleast_2d(
np.loadtxt(
os.path.join(cfg.working_dir, 'accepted_orientations.dat')))
n_quats = len(quats)
n_jobs = 0
phi, n = angleAxisOfRotMat(rotMatOfQuat(quats.T))
for i, (phi, n) in enumerate(zip(phi, n.T)):
if ids_to_refine is None or i in ids_to_refine:
exp_map = phi * n
grain_params = np.hstack(
[exp_map, 0., 0., 0., 1., 1., 1., 0., 0., 0.])
job_queue.put((i, grain_params))
n_jobs += 1
logger.info("fitting grains for %d of %d orientations", n_jobs, n_quats)
return job_queue, n_jobs
def objFunc(x, grainList, scl):
"""
"""
x = x / scl # remove scaling
xc = x[0] # beam x-center
zTilt = x[1] # zTilt --> inclination of oscill. axis on detector
chiTilt = x[2] # zTilt --> inclination of oscill. axis on detector
for i in range(len(grainList)):
grainList[i].detectorGeom.xc = xc
grainList[i].detectorGeom.zTilt = zTilt
grainList[i].detectorGeom.chiTilt = chiTilt
# need a fresh detector object to hand to spots
# use first grain by default (any will do)
tmpDG = grainList[0].detectorGeom.makeNew()
tmpDG.pVec = None
# reset the detector used by all spots
# each grain currently carried th
# ...PRIME CANDIDATE FOR OPTIMIZATION/CLEANUP/GENERALIZATION...
# ...perhaps loop over only the spots used by the grains in grainList?...
# grainList[0].spots.resetDetectorGeom(tmpDG)
# strip out quantities to hand off to the fit objective fuction to get residual contribution
resd = []
for i in range(len(grainList)):
spotIDs = grainList[i].grainSpots['iRefl']
spotIDs = spotIDs[spotIDs >= 0]
for j in range(len(spotIDs)):
spot = grainList[i].spots._Spots__spots[spotIDs[j]]
spot.setDetectorGeom(tmpDG, clobber=True)
angCOM = spot.angCOM()
grainList[i].spots._Spots__spotAngCoords[spotIDs[j]] = angCOM
grainList[i].spots._Spots__spotXYOCoords[
spotIDs[j]] = grainList[i].spots.detectorGeom.angToXYO(*angCOM)
pass
# refit grains to new detector -- mainly for fixing pVecs
grainList[i].updateGVecs()
grainList[i].fit(display=False)
angAxs = ROT.angleAxisOfRotMat(grainList[i].rMat)
biotT = matrixutil.symmToVecMV(grainList[i].vMat - numpy.eye(3))
pVec = grainList[i].detectorGeom.pVec
x = numpy.vstack(
[angAxs[0] * angAxs[1],
biotT.reshape(6, 1),
pVec.reshape(3, 1)])
resd.append(grainList[i]._fitF_objFunc(x))
pass
resd = numpy.hstack(resd).flatten()
return sum(resd**2)
def get_job_queue(cfg, ids_to_refine=None):
job_queue = mp.JoinableQueue()
# load the queue
try:
# use an estimate of the grain parameters, if available
estimate_f = cfg.fit_grains.estimate
grain_params_list = np.atleast_2d(np.loadtxt(estimate_f))
n_quats = len(grain_params_list)
n_jobs = 0
for grain_params in grain_params_list:
grain_id = grain_params[0]
if ids_to_refine is None or grain_id in ids_to_refine:
job_queue.put((grain_id, grain_params[3:15]))
n_jobs += 1
logger.info(
'fitting grains using "%s" for the initial estimate',
estimate_f
)
except (ValueError, IOError):
# no estimate available, use orientations and defaults
logger.info('fitting grains using default initial estimate')
# ...make this an attribute in cfg?
analysis_id = '%s_%s' % (
cfg.analysis_name.strip().replace(' ', '-'),
cfg.material.active.strip().replace(' ', '-'),
)
# load quaternion file
quats = np.atleast_2d(
np.loadtxt(
os.path.join(
cfg.working_dir,
'accepted_orientations_%s.dat' % analysis_id
)
)
)
n_quats = len(quats)
n_jobs = 0
phi, n = angleAxisOfRotMat(rotMatOfQuat(quats.T))
for i, (phi, n) in enumerate(zip(phi, n.T)):
if ids_to_refine is None or i in ids_to_refine:
exp_map = phi*n
grain_params = np.hstack(
[exp_map, 0., 0., 0., 1., 1., 1., 0., 0., 0.]
)
job_queue.put((i, grain_params))
n_jobs += 1
logger.info("fitting grains for %d of %d orientations", n_jobs, n_quats)
return job_queue, n_jobs
def objFunc(x, grainList, scl):
"""
"""
x = x / scl # remove scaling
xc = x[0] # beam x-center
zTilt = x[1] # zTilt --> inclination of oscill. axis on detector
chiTilt = x[2] # zTilt --> inclination of oscill. axis on detector
for i in range(len(grainList)):
grainList[i].detectorGeom.xc = xc
grainList[i].detectorGeom.zTilt = zTilt
grainList[i].detectorGeom.chiTilt = chiTilt
# need a fresh detector object to hand to spots
# use first grain by default (any will do)
tmpDG = grainList[0].detectorGeom.makeNew()
tmpDG.pVec = None
# reset the detector used by all spots
# each grain currently carried th
# ...PRIME CANDIDATE FOR OPTIMIZATION/CLEANUP/GENERALIZATION...
# ...perhaps loop over only the spots used by the grains in grainList?...
# grainList[0].spots.resetDetectorGeom(tmpDG)
# strip out quantities to hand off to the fit objective fuction to get residual contribution
resd = []
for i in range(len(grainList)):
spotIDs = grainList[i].grainSpots['iRefl']
spotIDs = spotIDs[spotIDs >= 0]
for j in range(len(spotIDs)):
spot = grainList[i].spots._Spots__spots[spotIDs[j]]
spot.setDetectorGeom(tmpDG, clobber=True)
angCOM = spot.angCOM()
grainList[i].spots._Spots__spotAngCoords[spotIDs[j]] = angCOM
grainList[i].spots._Spots__spotXYOCoords[spotIDs[j]] = grainList[i].spots.detectorGeom.angToXYO( *angCOM )
pass
# refit grains to new detector -- mainly for fixing pVecs
grainList[i].updateGVecs()
grainList[i].fit(display=False)
angAxs = ROT.angleAxisOfRotMat(grainList[i].rMat)
biotT = matrixutil.symmToVecMV(grainList[i].vMat - numpy.eye(3))
pVec = grainList[i].detectorGeom.pVec
x = numpy.vstack([angAxs[0]*angAxs[1], biotT.reshape(6, 1), pVec.reshape(3, 1)])
resd.append(grainList[i]._fitF_objFunc(x))
pass
resd = numpy.hstack(resd).flatten()
return sum(resd**2)
distortion = (dFuncs.GE_41RT, detector.getParams(allParams=True)[6:])
tVec_d = tVec_d_from_old_parfile(geomParams, det_origin)
detector_params = np.hstack(
[geomParams[3:6, 0],
tVec_d.flatten(), 0.,
np.zeros(3)])
use_tth_max = parser.get('pull_spots', 'use_tth_max')
if use_tth_max.strip() == '1' or use_tth_max.strip().lower() == 'true':
excl = np.zeros_like(pd.exclusions, dtype=bool)
pd.exclusions = excl
excl = pd.getTTh() > detector.getTThMax()
pd.exclusions = excl
pass
phi, n = rot.angleAxisOfRotMat(rot.rotMatOfQuat(qbar))
if have_progBar:
widgets = [Bar('>'), ' ', ETA(), ' ', ReverseBar('<')]
pbar = ProgressBar(widgets=widgets, maxval=len(qbar.T)).start()
pass
print "pulling spots for %d orientations..." % len(qbar.T)
for iq, quat in enumerate(qbar.T):
if have_progBar:
pbar.update(iq)
exp_map = phi[iq] * n[:, iq]
grain_params = np.hstack(
[exp_map.flatten(), 0., 0., 0., 1., 1., 1., 0., 0., 0.])
sd = xrdutil.pullSpots(pd,
detector_params,
grain_params,
reader,
def gen_sk(fname, det_size, det_pt, eVec, beam_len, bVec, rMat_b, rMat_d,
rMat_s, rMat_c, tVec_d, tVec_s, tVec_c):
if isinstance(fname, file):
fid = f
else:
fid = open(fname + '.sk', 'w')
phi_b, n_b = rot.angleAxisOfRotMat(rMat_b)
phi_d, n_d = rot.angleAxisOfRotMat(rMat_d)
phi_s, n_s = rot.angleAxisOfRotMat(rMat_s)
phi_c, n_c = rot.angleAxisOfRotMat(rMat_c)
tVec_c_rot = np.dot(rMat_s, tVec_c).flatten()
tVec_c_l = tVec_s.flatten() + tVec_c_rot.flatten()
# for diffracted beam
Z_d = np.dot(rMat_d, Zl)
P1_d = np.c_[det_pt[0], det_pt[1], 0.].T
P1_l = np.dot(rMat_d, P1_d) + tVec_d
P3_l = 0.
tTh_Eta, gVec_l = detectorXYToGvec(np.c_[det_pt[0], det_pt[1]],
rMat_d,
rMat_s,
tVec_d,
tVec_s,
tVec_c,
beamVec=bVec.reshape(3, 1),
etaVec=eVec.reshape(3, 1))
dHat_l = np.dot(np.eye(3) - 2 * np.dot(gVec_l, gVec_l.T), bVec)
tTh_vec = np.cross(bVec.flatten(), dHat_l.flatten())
tTh = r2d * np.arccos(np.dot(bVec.T, dHat_l))
# eye_vec = np.dot(2*np.dot(Yl, Yl.T) - np.eye(3), tVec_d).flatten()
# look_vec = np.dot(np.eye(3) - 2*np.dot(Yl, Yl.T), tVec_d).flatten()
eye_vec = np.r_[15, 5, 10]
look_vec = np.r_[0, 0, -7]
axwgt_pt = 1.5
"""
-------------------------------------------------
PRINT THAT SHIT
-------------------------------------------------
"""
print >> fid, '% -*-python-*-\n'
print >> fid, 'def n_segs 180'
print >> fid, 'def eye (%f, %f, %f)' % tuple(eye_vec)
print >> fid, 'def look_at (%f, %f, %f)' % tuple(look_vec)
print >> fid, 'def b0 (0, 0, %f)' % (beam_len)
print >> fid, 'def b1 (0, 0, %f)' % (-beam_len)
print >> fid, 'def bpt (%f, %f, %f)' % tuple(1.25 * bVec)
print >> fid, 'def bptd_p (%f, %f, %f)' % tuple(1.5 * bVec.flatten())
print >> fid, 'def bptd_m (%f, %f, %f)' % tuple(-1.5 * bVec.flatten())
print >> fid, 'def bvp (%f, %f, %f)' % tuple(bVec)
print >> fid, 'def evp (%f, %f, %f)' % tuple(eVec)
print >> fid, 'def p1 (0,0,0)'
print >> fid, 'def d1 (%f, %f, %f)' % tuple(P1_l.flatten())
print >> fid, 'def d2 (%f, %f, %f)' % tuple(1.25 * dHat_l.flatten() +
tVec_c_l.flatten())
print >> fid, 'def t2 (%f, %f, %f)' % tuple(tTh_vec.flatten() +
tVec_c_l.flatten())
print >> fid, 'def g1 (%f, %f, %f)' % tuple(gVec_l.flatten())
print >> fid, '\n% detector'
print >> fid, 'def tvec_d [%f, %f, %f]' % tuple(tVec_d.flatten())
print >> fid, 'def tpt_d (%f, %f, %f)' % tuple(tVec_d.flatten())
print >> fid, 'def tpt_d_label (%f, %f, %f)' % tuple(
0.5 * tVec_d.flatten())
print >> fid, '\n% sample'
print >> fid, 'def tvec_s [%f, %f, %f]' % tuple(tVec_s.flatten())
print >> fid, 'def tpt_s (%f, %f, %f)' % tuple(tVec_s.flatten())
print >> fid, 'def tpt_s_label (%f, %f, %f)' % tuple(
0.5 * tVec_s.flatten())
print >> fid, 'def chi %f' % (r2d * chi)
print >> fid, 'def ome %f' % (r2d * ome)
print >> fid, '\n% crystal'
print >> fid, 'def tvec_c [%f, %f, %f]' % tuple(tVec_c_rot)
print >> fid, 'def tpt_c (%f, %f, %f)' % tuple(tVec_c_l)
print >> fid, 'def tpt_c_label (%f, %f, %f)' % tuple(
0.5 * (tVec_c_l.flatten() + tVec_s.flatten()))
print >> fid, 'def tvec_c_l [%f, %f, %f]' % tuple(tVec_c_l)
print >> fid, 'def tthvec [%f, %f, %f]' % tuple(tTh_vec)
print >> fid, 'def tth %f' % (tTh)
print >> fid, 'def g1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() +
0.8 * gVec_l.flatten())
print >> fid, 'def b1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() +
1.2 * bVec.flatten())
print >> fid, 'def e1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() +
0.8 * eVec.flatten())
print >> fid, 'def chi_label (%f, %f, %f)' % tuple(tVec_s.flatten() +
np.r_[0, 1, 0.3])
print >> fid, 'def ome_label (%f, %f, %f)' % tuple(tVec_s.flatten() +
0.6 * np.r_[1, 0, -1])
print >> fid, 'def axlen 1.5'
print >> fid, 'def det_ang %f' % (r2d * phi_d)
print >> fid, 'def det_axis [%f, %f, %f]' % tuple(n_d)
print >> fid, 'def det_size_x %f' % (det_size[0])
print >> fid, 'def det_size_y %f' % (det_size[1])
print >> fid, 'def sam_ang %f' % (r2d * phi_s)
print >> fid, 'def sam_axis [%f, %f, %f]' % tuple(n_s)
print >> fid, 'def xtl_ang %f' % (r2d * phi_c)
print >> fid, 'def xtl_axis [%f, %f, %f]' % tuple(n_c)
print >> fid, '\n% the lab frame'
print >> fid, \
'def lab_frame { \n' + \
' line [linewidth=%fpt,arrows=->] (p1)(axlen,0,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' line [arrows=->,linecolor=cyan, lay=over] (p1)(evp) \n' + \
' line [arrows=->,linecolor=magenta] (p1)(bvp) \n' + \
' special |\uput[d ]#1{$\hat{\mathbf{X}}_l$} \n' + \
' \uput[u ]#2{$\hat{\mathbf{Y}}_l$} \n' + \
' \uput[u ]#3{$\hat{\mathbf{Z}}_l$} \n' + \
' \uput[dl]#4{$\hat{\mathbf{e}}$} \n' + \
' \uput[u ]#5{$\hat{\mathbf{b}}$} \n' + \
' \uput[d ]#6{$\mathrm{P}_0$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(1,0,0)(0,0,-1.2)(p1) \n' + \
' % put { rotate(beam_ang, (p1), [beam_axis]) } \n' + \
' % { line [linewidth=.2pt,linecolor=blue,linestyle=dashed] \n' + \
' % (b0)(b1) } \n' + \
' line [linewidth=.2pt,linecolor=blue,linestyle=dashed] (b0)(b1)\n' + \
' } \n'
print >> fid, '\n% the detector'
print >> fid, \
'def detector_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[d]#1{$\hat{\mathbf{X}}_d$} \n' + \
' \uput[r]#2{$\hat{\mathbf{Y}}_d$} \n' + \
' \uput[l]#3{$\hat{\mathbf{Z}}_d$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen) \n' + \
' polygon [fillcolor=gray, lay=under, linecolor=black] \n' + \
' (-0.5*det_size_x, -0.5*det_size_y) ( 0.5*det_size_x, -0.5*det_size_y) \n' + \
' ( 0.5*det_size_x, 0.5*det_size_y) (-0.5*det_size_x, 0.5*det_size_y) \n' + \
' line [linewidth=.2pt,linecolor=red,linestyle=dashed] (0, -0.6*det_size_y)(0, 0.6*det_size_y)\n' + \
' line [linewidth=.2pt,linecolor=red,linestyle=dashed] (-0.6*det_size_x, 0)(0.6*det_size_x, 0)\n' + \
' } \n'
print >> fid, '\n% the sample frame'
print >> fid, \
'def sample_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[dr]#1{$\hat{\mathbf{X}}_s$} \n' + \
' \uput[u ]#2{$\hat{\mathbf{Y}}_s$} \n' + \
' \uput[dr]#3{$\hat{\mathbf{Z}}_s$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(0,0,-1) \n' + \
' } \n'
print >> fid, '\n% the crystal frame'
print >> fid, \
'def crystal_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[r ]#1{$\hat{\mathbf{X}}_c$} \n' + \
' \uput[l ]#2{$\hat{\mathbf{Y}}_c$} \n' + \
' \uput[r ]#3{$\hat{\mathbf{Z}}_c$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(0,0,-1) \n' + \
' } \n'
print >> fid, '\n% transform and place objects'
print >> fid, \
'def final_detector { \n' + \
' put { rotate(det_ang, (p1), [det_axis]) then translate([tvec_d])} {detector_frame} \n' + \
' line [arrows=->,linecolor=red] (p1)(tpt_d) \n' + \
' special |\uput[dr]#1{$\mathrm{P}_1$} \n' + \
' \uput[ul]#2{$\mathbf{t}_d$} \n' + \
' \uput[l ]#3{$\mathrm{P}_4$}| \n' + \
' (tpt_d)(tpt_d_label)(d1) \n' + \
'} \n' + \
'def final_sample { \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s])} {sample_frame} \n' + \
' line [lay=over,arrows=->,linecolor=green] (p1)(tpt_s) \n' + \
' put { translate([tvec_s])} \n' + \
' { line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (0, -1.1*axlen, 0)(0, 1.1*axlen, 0) \n' + \
' line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (-1.1*axlen, 0, 0)(1.1*axlen, 0, 0) \n' + \
' line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (0, 0, -1.1*axlen)(0, 0, 1.1*axlen) } \n' + \
' put { translate([tvec_s]) } { \n' + \
' sweep[linecolor=black,arrows=->]{ \n' + \
' n_segs, rotate(chi/n_segs, (p1), [1,0,0])}(0,1,0) } \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s]) } { \n' + \
' { sweep[lay=over,linecolor=black,arrows=<-]{ \n' + \
' n_segs, rotate(-ome/n_segs, (p1), [0,1,0])}(1,0,0) } \n' + \
' { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' n_segs<>, rotate(360/n_segs, (p1), [0,1,0])}(0,0,1) } } \n' + \
' put { translate([tvec_s]) } { \n' + \
' % { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' % n_segs<>, rotate(360/n_segs, (p1), [0,1,0])}(0,0,1) } \n' + \
' { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' n_segs<>, rotate(360/n_segs, (p1), [1,0,0])}(0,0,1) } } \n' + \
' special |\uput[dl]#1{$\mathrm{P}_2$} \n' + \
' \uput[dr]#2{$\mathbf{t}_s$} \n' + \
' \uput[r ]#3{$\omega$} \n' + \
' \uput[l ]#4{$\chi$}| \n' + \
' (tpt_s)(tpt_s_label)(ome_label)(chi_label) \n' + \
'} \n' + \
'def final_crystal { \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s]) \n' + \
' then rotate(xtl_ang, (tpt_s), [xtl_axis]) then translate([tvec_c]) } { \n' + \
' {crystal_frame} } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=cyan] (p1)(evp) } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=magenta] (p1)(bvp) } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=gray] (p1)(g1) } \n' + \
' line [arrows=->,linecolor=blue] (tpt_s)(tpt_c) \n' + \
' line [lay=over,arrows=->,linecolor=yellow] (tpt_c)(d1) \n' + \
' put { translate([tvec_c_l]) } { \n' + \
' { sweep[linecolor=black,arrows=->]{ \n' + \
' n_segs, rotate(tth/n_segs, (p1), [tthvec])}(bpt) } \n' + \
' { line[linewidth=0.2pt,linecolor=magenta,linestyle=dashed](bptd_m)(bptd_p)} } \n' + \
' special |\uput[u ]#1{$\hat{\mathbf{G}}$} \n' + \
' \uput[r ]#2{$\hat{\mathbf{e}}$} \n' + \
' \uput[r ]#3{$\hat{\mathbf{b}}$} \n' + \
' \uput[dr]#4{$\mathrm{P}_3$} \n' + \
' \uput[ r]#5{$\mathbf{t}_c$} \n' + \
' \uput[ur]#6{$2\\theta$}| \n' + \
' (g1_label)(e1_label)(b1_label)(tpt_c)(tpt_c_label)(d2) \n' + \
'} \n' + \
' \n' + \
'put { view((eye), (look_at)) } { {lab_frame} {final_detector} {final_sample} {final_crystal} }\n'
fid.close()
geomParams = np.vstack([detector.getParams(allParams=True)[:6],
np.zeros(6)]).T
distortion = (dFuncs.GE_41RT, detector.getParams(allParams=True)[6:])
tVec_d = tVec_d_from_old_parfile(geomParams, det_origin)
detector_params = np.hstack([geomParams[3:6, 0], tVec_d.flatten(), 0., np.zeros(3)])
use_tth_max = parser.get('pull_spots', 'use_tth_max')
if use_tth_max.strip() == '1' or use_tth_max.strip().lower() == 'true':
excl = np.zeros_like(pd.exclusions, dtype=bool)
pd.exclusions = excl
excl = pd.getTTh() > detector.getTThMax()
pd.exclusions = excl
pass
phi, n = rot.angleAxisOfRotMat(rot.rotMatOfQuat(qbar))
if have_progBar:
widgets = [Bar('>'), ' ', ETA(), ' ', ReverseBar('<')]
pbar = ProgressBar(widgets=widgets, maxval=len(qbar.T)).start()
pass
print "pulling spots for %d orientations..." %len(qbar.T)
for iq, quat in enumerate(qbar.T):
if have_progBar:
pbar.update(iq)
exp_map = phi[iq]*n[:, iq]
grain_params = np.hstack([exp_map.flatten(), 0., 0., 0., 1., 1., 1., 0., 0., 0.])
sd = xrdutil.pullSpots(pd, detector_params, grain_params, reader,
filename=pull_filename %iq,
eta_range=etaRange, ome_period=ome_period,
eta_tol=eta_tol, ome_tol=ome_tol,
threshold=pthresh, tth_tol=tth_tol,
def gen_sk(fname, det_size, det_pt, eVec,
beam_len, bVec, rMat_b,
rMat_d, rMat_s, rMat_c,
tVec_d, tVec_s, tVec_c):
if isinstance(fname, file):
fid = f
else:
fid = open(fname + '.sk', 'w')
phi_b, n_b = rot.angleAxisOfRotMat(rMat_b)
phi_d, n_d = rot.angleAxisOfRotMat(rMat_d)
phi_s, n_s = rot.angleAxisOfRotMat(rMat_s)
phi_c, n_c = rot.angleAxisOfRotMat(rMat_c)
tVec_c_rot = np.dot(rMat_s, tVec_c).flatten()
tVec_c_l = tVec_s.flatten() + tVec_c_rot.flatten()
# for diffracted beam
Z_d = np.dot(rMat_d, Zl)
P1_d = np.c_[det_pt[0], det_pt[1], 0.].T
P1_l = np.dot(rMat_d, P1_d) + tVec_d
P3_l = 0.
tTh_Eta, gVec_l = detectorXYToGvec(np.c_[det_pt[0], det_pt[1]],
rMat_d, rMat_s,
tVec_d, tVec_s, tVec_c,
beamVec=bVec.reshape(3, 1),
etaVec=eVec.reshape(3, 1))
dHat_l = np.dot(np.eye(3) - 2*np.dot(gVec_l, gVec_l.T), bVec)
tTh_vec = np.cross(bVec.flatten(), dHat_l.flatten())
tTh = r2d*np.arccos(np.dot(bVec.T, dHat_l))
# eye_vec = np.dot(2*np.dot(Yl, Yl.T) - np.eye(3), tVec_d).flatten()
# look_vec = np.dot(np.eye(3) - 2*np.dot(Yl, Yl.T), tVec_d).flatten()
eye_vec = np.r_[15, 5, 10]
look_vec = np.r_[0, 0, -7]
axwgt_pt = 1.5
"""
-------------------------------------------------
PRINT THAT SHIT
-------------------------------------------------
"""
print >> fid, '% -*-python-*-\n'
print >> fid, 'def n_segs 180'
print >> fid, 'def eye (%f, %f, %f)' % tuple(eye_vec)
print >> fid, 'def look_at (%f, %f, %f)' % tuple(look_vec)
print >> fid, 'def b0 (0, 0, %f)' % (beam_len)
print >> fid, 'def b1 (0, 0, %f)' % (-beam_len)
print >> fid, 'def bpt (%f, %f, %f)' % tuple(1.25*bVec)
print >> fid, 'def bptd_p (%f, %f, %f)' % tuple(1.5*bVec.flatten())
print >> fid, 'def bptd_m (%f, %f, %f)' % tuple(-1.5*bVec.flatten())
print >> fid, 'def bvp (%f, %f, %f)' % tuple(bVec)
print >> fid, 'def evp (%f, %f, %f)' % tuple(eVec)
print >> fid, 'def p1 (0,0,0)'
print >> fid, 'def d1 (%f, %f, %f)' % tuple(P1_l.flatten())
print >> fid, 'def d2 (%f, %f, %f)' % tuple(1.25*dHat_l.flatten() + tVec_c_l.flatten())
print >> fid, 'def t2 (%f, %f, %f)' % tuple(tTh_vec.flatten() + tVec_c_l.flatten())
print >> fid, 'def g1 (%f, %f, %f)' % tuple(gVec_l.flatten())
print >> fid, '\n% detector'
print >> fid, 'def tvec_d [%f, %f, %f]' % tuple(tVec_d.flatten())
print >> fid, 'def tpt_d (%f, %f, %f)' % tuple(tVec_d.flatten())
print >> fid, 'def tpt_d_label (%f, %f, %f)' % tuple(0.5*tVec_d.flatten())
print >> fid, '\n% sample'
print >> fid, 'def tvec_s [%f, %f, %f]' % tuple(tVec_s.flatten())
print >> fid, 'def tpt_s (%f, %f, %f)' % tuple(tVec_s.flatten())
print >> fid, 'def tpt_s_label (%f, %f, %f)' % tuple(0.5*tVec_s.flatten())
print >> fid, 'def chi %f' % (r2d*chi)
print >> fid, 'def ome %f' % (r2d*ome)
print >> fid, '\n% crystal'
print >> fid, 'def tvec_c [%f, %f, %f]' % tuple(tVec_c_rot)
print >> fid, 'def tpt_c (%f, %f, %f)' % tuple(tVec_c_l)
print >> fid, 'def tpt_c_label (%f, %f, %f)' % tuple(0.5*(tVec_c_l.flatten() + tVec_s.flatten()))
print >> fid, 'def tvec_c_l [%f, %f, %f]' % tuple(tVec_c_l)
print >> fid, 'def tthvec [%f, %f, %f]' % tuple(tTh_vec)
print >> fid, 'def tth %f' % (tTh)
print >> fid, 'def g1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() + 0.8*gVec_l.flatten())
print >> fid, 'def b1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() + 1.2*bVec.flatten())
print >> fid, 'def e1_label (%f, %f, %f)' % tuple(tVec_c_l.flatten() + 0.8*eVec.flatten())
print >> fid, 'def chi_label (%f, %f, %f)' % tuple(tVec_s.flatten() + np.r_[0, 1, 0.3])
print >> fid, 'def ome_label (%f, %f, %f)' % tuple(tVec_s.flatten() + 0.6*np.r_[1, 0, -1])
print >> fid, 'def axlen 1.5'
print >> fid, 'def det_ang %f' % (r2d*phi_d)
print >> fid, 'def det_axis [%f, %f, %f]' % tuple(n_d)
print >> fid, 'def det_size_x %f'% (det_size[0])
print >> fid, 'def det_size_y %f'% (det_size[1])
print >> fid, 'def sam_ang %f' % (r2d*phi_s)
print >> fid, 'def sam_axis [%f, %f, %f]' % tuple(n_s)
print >> fid, 'def xtl_ang %f' % (r2d*phi_c)
print >> fid, 'def xtl_axis [%f, %f, %f]' % tuple(n_c)
print >> fid, '\n% the lab frame'
print >> fid, \
'def lab_frame { \n' + \
' line [linewidth=%fpt,arrows=->] (p1)(axlen,0,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' line [arrows=->,linecolor=cyan, lay=over] (p1)(evp) \n' + \
' line [arrows=->,linecolor=magenta] (p1)(bvp) \n' + \
' special |\uput[d ]#1{$\hat{\mathbf{X}}_l$} \n' + \
' \uput[u ]#2{$\hat{\mathbf{Y}}_l$} \n' + \
' \uput[u ]#3{$\hat{\mathbf{Z}}_l$} \n' + \
' \uput[dl]#4{$\hat{\mathbf{e}}$} \n' + \
' \uput[u ]#5{$\hat{\mathbf{b}}$} \n' + \
' \uput[d ]#6{$\mathrm{P}_0$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(1,0,0)(0,0,-1.2)(p1) \n' + \
' % put { rotate(beam_ang, (p1), [beam_axis]) } \n' + \
' % { line [linewidth=.2pt,linecolor=blue,linestyle=dashed] \n' + \
' % (b0)(b1) } \n' + \
' line [linewidth=.2pt,linecolor=blue,linestyle=dashed] (b0)(b1)\n' + \
' } \n'
print >> fid, '\n% the detector'
print >> fid, \
'def detector_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[d]#1{$\hat{\mathbf{X}}_d$} \n' + \
' \uput[r]#2{$\hat{\mathbf{Y}}_d$} \n' + \
' \uput[l]#3{$\hat{\mathbf{Z}}_d$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen) \n' + \
' polygon [fillcolor=gray, lay=under, linecolor=black] \n' + \
' (-0.5*det_size_x, -0.5*det_size_y) ( 0.5*det_size_x, -0.5*det_size_y) \n' + \
' ( 0.5*det_size_x, 0.5*det_size_y) (-0.5*det_size_x, 0.5*det_size_y) \n' + \
' line [linewidth=.2pt,linecolor=red,linestyle=dashed] (0, -0.6*det_size_y)(0, 0.6*det_size_y)\n' + \
' line [linewidth=.2pt,linecolor=red,linestyle=dashed] (-0.6*det_size_x, 0)(0.6*det_size_x, 0)\n' + \
' } \n'
print >> fid, '\n% the sample frame'
print >> fid, \
'def sample_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[dr]#1{$\hat{\mathbf{X}}_s$} \n' + \
' \uput[u ]#2{$\hat{\mathbf{Y}}_s$} \n' + \
' \uput[dr]#3{$\hat{\mathbf{Z}}_s$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(0,0,-1) \n' + \
' } \n'
print >> fid, '\n% the crystal frame'
print >> fid, \
'def crystal_frame { \n' + \
' line [linewidth=%fpt,arrows=<->] (axlen,0,0)(p1)(0,axlen,0) \n' % (axwgt_pt) + \
' line [linewidth=%fpt,arrows=->] (p1)(0,0,axlen) \n' % (axwgt_pt) + \
' special |\uput[r ]#1{$\hat{\mathbf{X}}_c$} \n' + \
' \uput[l ]#2{$\hat{\mathbf{Y}}_c$} \n' + \
' \uput[r ]#3{$\hat{\mathbf{Z}}_c$}| \n' + \
' (axlen,0,0)(0,axlen,0)(0,0,axlen)(0,0,-1) \n' + \
' } \n'
print >> fid, '\n% transform and place objects'
print >> fid, \
'def final_detector { \n' + \
' put { rotate(det_ang, (p1), [det_axis]) then translate([tvec_d])} {detector_frame} \n' + \
' line [arrows=->,linecolor=red] (p1)(tpt_d) \n' + \
' special |\uput[dr]#1{$\mathrm{P}_1$} \n' + \
' \uput[ul]#2{$\mathbf{t}_d$} \n' + \
' \uput[l ]#3{$\mathrm{P}_4$}| \n' + \
' (tpt_d)(tpt_d_label)(d1) \n' + \
'} \n' + \
'def final_sample { \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s])} {sample_frame} \n' + \
' line [lay=over,arrows=->,linecolor=green] (p1)(tpt_s) \n' + \
' put { translate([tvec_s])} \n' + \
' { line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (0, -1.1*axlen, 0)(0, 1.1*axlen, 0) \n' + \
' line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (-1.1*axlen, 0, 0)(1.1*axlen, 0, 0) \n' + \
' line [lay=over,linewidth=.2pt,linecolor=green,linestyle=dashed] \n' + \
' (0, 0, -1.1*axlen)(0, 0, 1.1*axlen) } \n' + \
' put { translate([tvec_s]) } { \n' + \
' sweep[linecolor=black,arrows=->]{ \n' + \
' n_segs, rotate(chi/n_segs, (p1), [1,0,0])}(0,1,0) } \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s]) } { \n' + \
' { sweep[lay=over,linecolor=black,arrows=<-]{ \n' + \
' n_segs, rotate(-ome/n_segs, (p1), [0,1,0])}(1,0,0) } \n' + \
' { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' n_segs<>, rotate(360/n_segs, (p1), [0,1,0])}(0,0,1) } } \n' + \
' put { translate([tvec_s]) } { \n' + \
' % { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' % n_segs<>, rotate(360/n_segs, (p1), [0,1,0])}(0,0,1) } \n' + \
' { sweep[fillstyle=none,linecolor=black,linestyle=dashed,linewidth=0.2pt]{ \n' + \
' n_segs<>, rotate(360/n_segs, (p1), [1,0,0])}(0,0,1) } } \n' + \
' special |\uput[dl]#1{$\mathrm{P}_2$} \n' + \
' \uput[dr]#2{$\mathbf{t}_s$} \n' + \
' \uput[r ]#3{$\omega$} \n' + \
' \uput[l ]#4{$\chi$}| \n' + \
' (tpt_s)(tpt_s_label)(ome_label)(chi_label) \n' + \
'} \n' + \
'def final_crystal { \n' + \
' put { rotate(sam_ang, (p1), [sam_axis]) then translate([tvec_s]) \n' + \
' then rotate(xtl_ang, (tpt_s), [xtl_axis]) then translate([tvec_c]) } { \n' + \
' {crystal_frame} } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=cyan] (p1)(evp) } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=magenta] (p1)(bvp) } \n' + \
' put { translate([tvec_c_l]) } { line [arrows=->,linecolor=gray] (p1)(g1) } \n' + \
' line [arrows=->,linecolor=blue] (tpt_s)(tpt_c) \n' + \
' line [lay=over,arrows=->,linecolor=yellow] (tpt_c)(d1) \n' + \
' put { translate([tvec_c_l]) } { \n' + \
' { sweep[linecolor=black,arrows=->]{ \n' + \
' n_segs, rotate(tth/n_segs, (p1), [tthvec])}(bpt) } \n' + \
' { line[linewidth=0.2pt,linecolor=magenta,linestyle=dashed](bptd_m)(bptd_p)} } \n' + \
' special |\uput[u ]#1{$\hat{\mathbf{G}}$} \n' + \
' \uput[r ]#2{$\hat{\mathbf{e}}$} \n' + \
' \uput[r ]#3{$\hat{\mathbf{b}}$} \n' + \
' \uput[dr]#4{$\mathrm{P}_3$} \n' + \
' \uput[ r]#5{$\mathbf{t}_c$} \n' + \
' \uput[ur]#6{$2\\theta$}| \n' + \
' (g1_label)(e1_label)(b1_label)(tpt_c)(tpt_c_label)(d2) \n' + \
'} \n' + \
' \n' + \
'put { view((eye), (look_at)) } { {lab_frame} {final_detector} {final_sample} {final_crystal} }\n'
fid.close()