def matchOmegas(xyo_det, hkls_idx, chi, rMat_c, bMat, wavelength,
vInv=vInv_ref, beamVec=bVec_ref, etaVec=eta_ref,
omePeriod=None):
"""
For a given list of (x, y, ome) points, outputs the index into the results from
oscillAnglesOfHKLs, including the calculated omega values.
"""
# get omegas for rMat_s calculation
if omePeriod is not None:
meas_omes = xf.mapAngle(xyo_det[:, 2], omePeriod)
else:
meas_omes = xyo_det[:, 2]
oangs0, oangs1 = xf.oscillAnglesOfHKLs(hkls_idx, chi, rMat_c, bMat, wavelength,
vInv=vInv,
beamVec=beamVec,
etaVec=etaVec)
if omePeriod is not None:
calc_omes = np.vstack( [xf.mapAngle(oangs0[2, :], omePeriod),
xf.mapAngle(oangs1[2, :], omePeriod) ] )
else:
calc_omes = np.vstack( [xf.mapAngle(oangs0[2, :]),
xf.mapAngle(oangs1[2, :]) ] )
match_omes = np.argsort(abs(np.tile(meas_omes, (2, 1)) - calc_omes), axis=0) == 0
calc_omes = calc_omes.T.flatten()[match_omes.T.flatten()]
return match_omes, calc_omes
def matchOmegas(xyo_det, hkls_idx, chi, rMat_c, bMat, wavelength,
vInv=vInv_ref, beamVec=bVec_ref, etaVec=eta_ref,
omePeriod=None):
"""
For a given list of (x, y, ome) points, outputs the index into the results from
oscillAnglesOfHKLs, including the calculated omega values.
"""
# get omegas for rMat_s calculation
if omePeriod is not None:
meas_omes = xf.mapAngle(xyo_det[:, 2], omePeriod)
else:
meas_omes = xyo_det[:, 2]
oangs0, oangs1 = xfcapi.oscillAnglesOfHKLs(hkls_idx.T, chi, rMat_c, bMat, wavelength,
vInv=vInv,
beamVec=beamVec,
etaVec=etaVec)
if np.any(np.isnan(oangs0)):
nanIdx = np.where(np.isnan(oangs0[:, 0]))[0]
errorString = "Infeasible parameters for hkls:\n"
for i in range(len(nanIdx)):
errorString += "%d %d %d\n" % tuple(hkls_idx[:, nanIdx[i]])
raise RuntimeError, errorString
else:
# CAPI version gives vstacked angles... must be (2, nhkls)
calc_omes = np.vstack([oangs0[:, 2], oangs1[:, 2]])
if omePeriod is not None:
calc_omes = np.vstack([xf.mapAngle(oangs0[:, 2], omePeriod),
xf.mapAngle(oangs1[:, 2], omePeriod)])
# do angular difference
diff_omes = xf.angularDifference(np.tile(meas_omes, (2, 1)), calc_omes)
match_omes = np.argsort(diff_omes, axis=0) == 0
calc_omes = calc_omes.T.flatten()[match_omes.T.flatten()]
return match_omes, calc_omes
def matchOmegas(xyo_det, hkls_idx, chi, rMat_c, bMat, wavelength,
vInv=vInv_ref, beamVec=bVec_ref, etaVec=eta_ref,
omePeriod=None):
"""
For a given list of (x, y, ome) points, outputs the index into the results from
oscillAnglesOfHKLs, including the calculated omega values.
"""
# get omegas for rMat_s calculation
if omePeriod is not None:
meas_omes = xf.mapAngle(xyo_det[:, 2], omePeriod)
else:
meas_omes = xyo_det[:, 2]
oangs0, oangs1 = xfcapi.oscillAnglesOfHKLs(hkls_idx.T, chi, rMat_c, bMat, wavelength,
vInv=vInv,
beamVec=beamVec,
etaVec=etaVec)
if np.any(np.isnan(oangs0)):
nanIdx = np.where(np.isnan(oangs0[:, 0]))[0]
errorString = "Infeasible parameters for hkls:\n"
for i in range(len(nanIdx)):
errorString += "%d %d %d\n" % tuple(hkls_idx[:, nanIdx[i]])
raise RuntimeError, errorString
else:
# CAPI version gives vstacked angles... must be (2, nhkls)
calc_omes = np.vstack([oangs0[:, 2], oangs1[:, 2]])
if omePeriod is not None:
calc_omes = np.vstack([xf.mapAngle(oangs0[:, 2], omePeriod),
xf.mapAngle(oangs1[:, 2], omePeriod)])
# do angular difference
diff_omes = xf.angularDifference(np.tile(meas_omes, (2, 1)), calc_omes)
match_omes = np.argsort(diff_omes, axis=0) == 0
calc_omes = calc_omes.T.flatten()[match_omes.T.flatten()]
return match_omes, calc_omes
def calibrateDetectorFromSX(xyo_det, hkls_idx, bMat, wavelength,
tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
vInv=vInv_ref,
beamVec=bVec_ref, etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref, dFlag_ref, dScl_ref),
pFlag=pFlag_ref, pScl=pScl_ref,
omePeriod=None,
factor=0.1, xtol=1e-8, ftol=1e-8):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
dFunc = distortion[0]
dParams = distortion[1]
dFlag = distortion[2]
dScl = distortion[3]
# p = np.zeros(16)
#
# p[0] = tiltAngles[0]
# p[1] = tiltAngles[1]
# p[2] = tiltAngles[2]
# p[3] = tVec_d[0]
# p[4] = tVec_d[1]
# p[5] = tVec_d[2]
# p[6] = chi
# p[7] = tVec_s[0]
# p[8] = tVec_s[1]
# p[9] = tVec_s[2]
# p[10] = expMap_c[0]
# p[11] = expMap_c[1]
# p[12] = expMap_c[2]
# p[13] = tVec_c[0]
# p[14] = tVec_c[1]
# p[15] = tVec_c[2]
#
# pFull = np.hstack([p, dParams])
pFull = geomParamsToInput(tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
dParams)
refineFlag = np.hstack([pFlag, dFlag])
scl = np.hstack([pScl, dScl])
pFit = pFull[refineFlag]
fitArgs = (pFull, pFlag, dFunc, dFlag, xyo_det, hkls_idx,
bMat, vInv, wavelength, beamVec, etaVec, omePeriod)
results = opt.leastsq(objFuncSX, pFit, args=fitArgs, diag=scl[refineFlag].flatten(),
factor=factor, xtol=xtol, ftol=ftol)
pFit_opt = results[0]
retval = pFull
retval[refineFlag] = pFit_opt
return retval
def calibrateDetectorFromSX(xyo_det, hkls_idx, bMat, wavelength,
tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
vInv=vInv_ref,
beamVec=bVec_ref, etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref, dFlag_ref, dScl_ref),
pFlag=pFlag_ref, pScl=pScl_ref,
omePeriod=None,
factor=0.1, xtol=1e-4, ftol=1e-4):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
dFunc = distortion[0]
dParams = distortion[1]
dFlag = distortion[2]
dScl = distortion[3]
# p = np.zeros(16)
#
# p[0] = tiltAngles[0]
# p[1] = tiltAngles[1]
# p[2] = tiltAngles[2]
# p[3] = tVec_d[0]
# p[4] = tVec_d[1]
# p[5] = tVec_d[2]
# p[6] = chi
# p[7] = tVec_s[0]
# p[8] = tVec_s[1]
# p[9] = tVec_s[2]
# p[10] = expMap_c[0]
# p[11] = expMap_c[1]
# p[12] = expMap_c[2]
# p[13] = tVec_c[0]
# p[14] = tVec_c[1]
# p[15] = tVec_c[2]
#
# pFull = np.hstack([p, dParams])
pFull = geomParamsToInput(tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
dParams)
refineFlag = np.hstack([pFlag, dFlag])
scl = np.hstack([pScl, dScl])
pFit = pFull[refineFlag]
fitArgs = (pFull, pFlag, dFunc, dFlag, xyo_det, hkls_idx,
bMat, vInv, wavelength, beamVec, etaVec, omePeriod)
results = optimize.leastsq(objFuncSX, pFit, args=fitArgs,
diag=1./scl[refineFlag].flatten(),
factor=factor, xtol=xtol, ftol=ftol)
pFit_opt = results[0]
retval = pFull
retval[refineFlag] = pFit_opt
return retval
def fit_grains(self, grain_id, grain_params):
"""
Executes lsq fits of grains based on spot files
REFLECTION TABLE
Cols as follows:
0-6: ID PID H K L sum(int) max(int)
6-9: pred tth pred eta pred ome
9-12: meas tth meas eta meas ome
12-15: meas X meas Y meas ome
"""
ome_start = self._p['omega_start']
ome_step = self._p['omega_step']
ome_stop = self._p['omega_stop']
refl_table = np.loadtxt(self._p['spots_stem'] % grain_id)
valid_refl_ids = refl_table[:, 0] >= 0
unsat_spots = refl_table[:, 6] < self._p['saturation_level']
pred_ome = refl_table[:, 9]
if angularDifference(ome_start, ome_stop, units='degrees') > 0:
# if here, incomplete have omega range and
# clip the refelctions very close to the edges to avoid
# problems with the least squares...
if np.sign(ome_step) < 0:
idx_ome = np.logical_and(
pred_ome < np.radians(ome_start + 2*ome_step),
pred_ome > np.radians(ome_stop - 2*ome_step)
)
else:
idx_ome = np.logical_and(
pred_ome > np.radians(ome_start + 2*ome_step),
pred_ome < np.radians(ome_stop - 2*ome_step)
)
idx = np.logical_and(
valid_refl_ids,
np.logical_and(unsat_spots, idx_ome)
)
else:
idx = np.logical_and(valid_refl_ids, unsat_spots)
hkls = refl_table[idx, 2:5].T # must be column vectors
self._p['hkls'] = hkls
xyo_det = refl_table[idx, -3:] # these are the cartesian centroids + ome
xyo_det[:, 2] = mapAngle(xyo_det[:, 2], self._p['omega_period'])
self._p['xyo_det'] = xyo_det
if sum(idx) <= 12:
return grain_params, 0
grain_params = fitGrain(
xyo_det, hkls, self._p['bMat'], self._p['wlen'],
self._p['detector_params'],
grain_params[:3], grain_params[3:6], grain_params[6:],
beamVec=bVec_ref, etaVec=eta_ref,
distortion=self._p['distortion'],
gFlag=gFlag, gScl=gScl,
omePeriod=self._p['omega_period']
)
completeness = sum(valid_refl_ids)/float(len(valid_refl_ids))
return grain_params, completeness
def fitGrain(
xyo_det,
hkls_idx,
bMat,
wavelength,
detectorParams,
expMap_c,
tVec_c,
vInv,
beamVec=bVec_ref,
etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref),
gFlag=gFlag_ref,
gScl=gScl_ref,
omePeriod=None,
factor=0.1,
xtol=1e-4,
ftol=1e-4,
):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
dFunc = distortion[0]
dParams = distortion[1]
gFull = np.hstack([expMap_c.flatten(), tVec_c.flatten(), vInv.flatten()])
gFit = gFull[gFlag]
fitArgs = (
gFull,
gFlag,
detectorParams,
xyo_det,
hkls_idx,
bMat,
wavelength,
beamVec,
etaVec,
dFunc,
dParams,
omePeriod,
)
results = optimize.leastsq(
objFuncFitGrain, gFit, args=fitArgs, diag=1.0 / gScl[gFlag].flatten(), factor=0.1, xtol=xtol, ftol=ftol
)
gFit_opt = results[0]
retval = gFull
retval[gFlag] = gFit_opt
return retval
def simulate_diffractions(grain_params, experiment, controller):
"""actual forward simulation of the diffraction"""
image_stack = np.zeros(
(experiment.nframes, experiment.nrows, experiment.ncols), dtype=bool)
count = len(grain_params)
subprocess = 'simulate diffractions'
_project = xrdutil._project_on_detector_plane
rD = experiment.rMat_d
chi = experiment.chi
tD = experiment.tVec_d
tS = experiment.tVec_s
distortion = experiment.distortion
eta_range = [
(-np.pi, np.pi),
]
ome_range = experiment.ome_range
ome_period = (-np.pi, np.pi)
full_hkls = xrdutil._fetch_hkls_from_planedata(experiment.plane_data)
bMat = experiment.plane_data.latVecOps['B']
wlen = experiment.plane_data.wavelength
controller.start(subprocess, count)
for i in range(count):
rC = xfcapi.makeRotMatOfExpMap(grain_params[i][0:3])
tC = np.ascontiguousarray(grain_params[i][3:6])
vInv_s = np.ascontiguousarray(grain_params[i][6:12])
ang_list = np.vstack(
xfcapi.oscillAnglesOfHKLs(full_hkls[:, 1:],
chi,
rC,
bMat,
wlen,
vInv=vInv_s))
# hkls not needed here
all_angs, _ = xrdutil._filter_hkls_eta_ome(full_hkls, ang_list,
eta_range, ome_range)
all_angs[:, 2] = xf.mapAngle(all_angs[:, 2], ome_period)
det_xy, _ = _project(all_angs, rD, rC, chi, tD, tC, tS, distortion)
_write_pixels(det_xy, all_angs[:, 2], image_stack, experiment.base,
experiment.inv_deltas, experiment.clip_vals)
controller.update(i + 1)
controller.finish(subprocess)
return image_stack
def fit_grains(self, grain_id, grain_params):
ome_start = self._p['omega_start']
ome_step = self._p['omega_step']
ome_stop = self._p['omega_stop']
refl_table = np.loadtxt(self._p['spots_stem'] % grain_id)
valid_refl_ids = refl_table[:, 0] >= 0
unsat_spots = refl_table[:, 5] < self._p['saturation_level']
pred_ome = refl_table[:, 8]
if angularDifference(ome_start, ome_stop, units='degrees') > 0:
# if here, incomplete have omega range and
# clip the refelctions very close to the edges to avoid
# problems with the least squares...
if np.sign(ome_step) < 0:
idx_ome = np.logical_and(
pred_ome < np.radians(ome_start + 2 * ome_step),
pred_ome > np.radians(ome_stop - 2 * ome_step))
else:
idx_ome = np.logical_and(
pred_ome > np.radians(ome_start + 2 * ome_step),
pred_ome < np.radians(ome_stop - 2 * ome_step))
idx = np.logical_and(unsat_spots,
np.logical_and(valid_refl_ids, idx_ome))
else:
idx = np.logical_and(valid_refl_ids, unsat_spots)
hkls = refl_table[idx, 1:4].T # must be column vectors
self._p['hkls'] = hkls
xyo_det = refl_table[idx,
-3:] # these are the cartesian centroids + ome
xyo_det[:, 2] = mapAngle(xyo_det[:, 2], self._p['omega_period'])
self._p['xyo_det'] = xyo_det
if sum(idx) <= 12:
return grain_params, 0
grain_params = fitGrain(xyo_det,
hkls,
self._p['bMat'],
self._p['wlen'],
self._p['detector_params'],
grain_params[:3],
grain_params[3:6],
grain_params[6:],
beamVec=bVec_ref,
etaVec=eta_ref,
distortion=self._p['distortion'],
gFlag=gFlag,
gScl=gScl,
omePeriod=self._p['omega_period'])
completeness = sum(idx) / float(len(idx))
return grain_params, completeness
def simulate_diffractions(grain_params, experiment, controller):
"""actual forward simulation of the diffraction"""
# use a packed array for the image_stack
array_dims = (experiment.nframes, experiment.ncols, ((experiment.nrows - 1)//8) + 1)
image_stack = np.zeros(array_dims, dtype = np.uint8)
count = len(grain_params)
subprocess = 'simulate diffractions'
_project = xrdutil._project_on_detector_plane
rD = experiment.rMat_d
chi = experiment.chi
tD = experiment.tVec_d
tS = experiment.tVec_s
distortion = experiment.distortion
eta_range = [(-np.pi, np.pi), ]
ome_range = experiment.ome_range
ome_period = (-np.pi, np.pi)
full_hkls = xrdutil._fetch_hkls_from_planedata(experiment.plane_data)
bMat = experiment.plane_data.latVecOps['B']
wlen = experiment.plane_data.wavelength
controller.start(subprocess, count)
for i in range(count):
rC = xfcapi.makeRotMatOfExpMap(grain_params[i][0:3])
tC = np.ascontiguousarray(grain_params[i][3:6])
vInv_s = np.ascontiguousarray(grain_params[i][6:12])
ang_list = np.vstack(xfcapi.oscillAnglesOfHKLs(full_hkls[:, 1:], chi,
rC, bMat, wlen,
vInv=vInv_s))
# hkls not needed here
all_angs, _ = xrdutil._filter_hkls_eta_ome(full_hkls, ang_list,
eta_range, ome_range)
all_angs[:, 2] =xf.mapAngle(all_angs[:, 2], ome_period)
det_xy, _ = _project(all_angs, rD, rC, chi, tD,
tC, tS, distortion)
_write_pixels(det_xy, all_angs[:,2], image_stack, experiment.base,
experiment.inv_deltas, experiment.clip_vals)
controller.update(i+1)
controller.finish(subprocess)
return image_stack
def fit_grains(self, grain_id, grain_params):
ome_start = self._p['omega_start']
ome_step = self._p['omega_step']
ome_stop = self._p['omega_stop']
refl_table = np.loadtxt(self._p['spots_stem'] % grain_id)
valid_refl_ids = refl_table[:, 0] >= 0
unsat_spots = refl_table[:, 5] < self._p['saturation_level']
pred_ome = refl_table[:, 8]
if angularDifference(ome_start, ome_stop, units='degrees') > 0:
# if here, incomplete have omega range and
# clip the refelctions very close to the edges to avoid
# problems with the least squares...
if np.sign(ome_step) < 0:
idx_ome = np.logical_and(
pred_ome < np.radians(ome_start + 2*ome_step),
pred_ome > np.radians(ome_stop - 2*ome_step)
)
else:
idx_ome = np.logical_and(
pred_ome > np.radians(ome_start + 2*ome_step),
pred_ome < np.radians(ome_stop - 2*ome_step)
)
idx = np.logical_and(
unsat_spots,
np.logical_and(valid_refl_ids, idx_ome)
)
else:
idx = np.logical_and(valid_refl_ids, unsat_spots)
hkls = refl_table[idx, 1:4].T # must be column vectors
self._p['hkls'] = hkls
xyo_det = refl_table[idx, -3:] # these are the cartesian centroids + ome
xyo_det[:, 2] = mapAngle(xyo_det[:, 2], self._p['omega_period'])
self._p['xyo_det'] = xyo_det
if sum(idx) <= 12:
return grain_params, 0
grain_params = fitGrain(
xyo_det, hkls, self._p['bMat'], self._p['wlen'],
self._p['detector_params'],
grain_params[:3], grain_params[3:6], grain_params[6:],
beamVec=bVec_ref, etaVec=eta_ref,
distortion=self._p['distortion'],
gFlag=gFlag, gScl=gScl,
omePeriod=self._p['omega_period']
)
completeness = sum(idx)/float(len(idx))
return grain_params, completeness
def fitGrain(xyo_det,
hkls_idx,
bMat,
wavelength,
detectorParams,
expMap_c,
tVec_c,
vInv,
beamVec=bVec_ref,
etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref),
gFlag=gFlag_ref,
gScl=gScl_ref,
omePeriod=None,
factor=0.1,
xtol=sqrt_epsf,
ftol=sqrt_epsf):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
dFunc = distortion[0]
dParams = distortion[1]
gFull = np.hstack([expMap_c.flatten(), tVec_c.flatten(), vInv.flatten()])
gFit = gFull[gFlag]
fitArgs = (gFull, gFlag, detectorParams, xyo_det, hkls_idx, bMat,
wavelength, beamVec, etaVec, dFunc, dParams, omePeriod)
results = optimize.leastsq(objFuncFitGrain,
gFit,
args=fitArgs,
diag=1. / gScl[gFlag].flatten(),
factor=0.1,
xtol=xtol,
ftol=ftol)
gFit_opt = results[0]
retval = gFull
retval[gFlag] = gFit_opt
return retval
def fit_grains(self, grain_id, grain_params):
ome_start = self._p['omega_start']
ome_step = self._p['omega_step']
ome_stop = self._p['omega_stop']
gtable = np.loadtxt(self._p['spots_stem'] % grain_id)
valid_refl_ids = gtable[:, 0] >= 0
pred_ome = gtable[:, 6]
if np.sign(ome_step) < 0:
idx_ome = np.logical_and(
pred_ome < np.radians(ome_start + 2*ome_step),
pred_ome > np.radians(ome_stop - 2*ome_step)
)
else:
idx_ome = np.logical_and(
pred_ome > np.radians(ome_start + 2*ome_step),
pred_ome < np.radians(ome_stop - 2*ome_step)
)
idx = np.logical_and(valid_refl_ids, idx_ome)
hkls = gtable[idx, 1:4].T # must be column vectors
self._p['hkls'] = hkls
xyo_det = gtable[idx, -3:] # these are the cartesian centroids + ome
xyo_det[:, 2] = mapAngle(xyo_det[:, 2], self._p['omega_period'])
self._p['xyo_det'] = xyo_det
if sum(idx) <= 12:
return grain_params, 0
grain_params = fitGrain(
xyo_det, hkls, self._p['bMat'], self._p['wlen'],
self._p['detector_params'],
grain_params[:3], grain_params[3:6], grain_params[6:],
beamVec=bVec_ref, etaVec=eta_ref,
distortion=self._p['distortion'],
gFlag=gFlag, gScl=gScl,
omePeriod=self._p['omega_period']
)
completeness = sum(idx)/float(len(idx))
return grain_params, completeness
def calibrateDetectorFromSX(
xyo_det, hkls_idx, bMat, wavelength,
tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
vInv=vInv_ref,
beamVec=bVec_ref, etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref, dFlag_ref, dScl_ref),
pFlag=pFlag_ref, pScl=pScl_ref,
omePeriod=None,
factor=0.1,
xtol=sqrt_epsf, ftol=sqrt_epsf):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
# FIXME: this format for distortion needs to go away ASAP <JVB 2017-03-27>
dFunc = distortion[0]
dParams = distortion[1]
dFlag = distortion[2]
dScl = distortion[3]
"""
p = np.zeros(17)
p[0] = wavelength
p[1] = tiltAngles[0]
p[2] = tiltAngles[1]
p[3] = tiltAngles[2]
p[4] = tVec_d[0]
p[5] = tVec_d[1]
p[6] = tVec_d[2]
p[7] = chi
p[8] = tVec_s[0]
p[9] = tVec_s[1]
p[10] = tVec_s[2]
p[11] = expMap_c[0]
p[12] = expMap_c[1]
p[13] = expMap_c[2]
p[14] = tVec_c[0]
p[15] = tVec_c[1]
p[16] = tVec_c[2]
pFull = np.hstack([p, dParams])
"""
pFull = geomParamsToInput(
wavelength,
tiltAngles, chi, expMap_c,
tVec_d, tVec_s, tVec_c,
dParams
)
# TODO: check scaling <JVB 2017-03-27>
refineFlag = np.array(np.hstack([pFlag, dFlag]), dtyp=bool)
scl = np.hstack([pScl, dScl])
pFit = pFull[refineFlag]
fitArgs = (pFull, pFlag, dFunc, dFlag, xyo_det, hkls_idx,
bMat, vInv, beamVec, etaVec, omePeriod)
results = optimize.leastsq(objFuncSX, pFit, args=fitArgs,
diag=1./scl[refineFlag].flatten(),
factor=factor, xtol=xtol, ftol=ftol)
pFit_opt = results[0]
retval = pFull
retval[refineFlag] = pFit_opt
return retval
for i in range(2):
gtable = np.loadtxt(filename %grainID) # load pull_spots output table
idx0 = gtable[:, 0] >= 0 # select valid reflections
#
pred_ome = gtable[:, 6]
if np.sign(ome_delta) < 0:
idx_ome = np.logical_and(pred_ome < d2r*(ome_start + 2*ome_delta),
pred_ome > d2r*(ome_stop - 2*ome_delta))
else:
idx_ome = np.logical_and(pred_ome > d2r*(ome_start + 2*ome_delta),
pred_ome < d2r*(ome_stop - 2*ome_delta))
#
idx = np.logical_and(idx0, idx_ome)
hkls = gtable[idx, 1:4].T # must be column vectors
xyo_det = gtable[idx, -3:] # these are the cartesian centroids + ome
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], ome_period)
print "completeness: %f%%" %(100. * sum(idx)/float(len(idx)))
if sum(idx) > 12:
g_initial = grain_params
g_refined = fitting.fitGrain(xyo_det, hkls, bMat, wlen,
detector_params,
g_initial[:3], g_initial[3:6], g_initial[6:],
beamVec=bVec_ref, etaVec=eta_ref,
distortion=(dFunc, dParams),
gFlag=gFlag, gScl=gScl,
omePeriod=ome_period)
if i == 0:
fid = open(filename %grainID, 'w')
sd = xrdutil.pullSpots(pd, detector_params, g_refined, reader,
distortion=(dFunc, dParams),
eta_range=etaRange, ome_period=ome_period,
def paintGridThis(quat):
"""
"""
# Unpack common parameters into locals
symHKLs = paramMP['symHKLs']
symHKLs_ix = paramMP['symHKLs_ix']
wavelength = paramMP['wavelength']
hklList = paramMP['hklList']
omeMin = paramMP['omeMin']
omeMax = paramMP['omeMax']
omeTol = paramMP['omeTol']
omePeriod = paramMP['omePeriod']
omeIndices = paramMP['omeIndices']
omeEdges = paramMP['omeEdges']
etaMin = paramMP['etaMin']
etaMax = paramMP['etaMax']
etaTol = paramMP['etaTol']
etaIndices = paramMP['etaIndices']
etaEdges = paramMP['etaEdges']
etaOmeMaps = paramMP['etaOmeMaps']
bMat = paramMP['bMat']
threshold = paramMP['threshold']
# need this for proper index generation
delOmeSign = num.sign(omeEdges[1] - omeEdges[0])
del_ome = abs(omeEdges[1] - omeEdges[0])
del_eta = abs(etaEdges[1] - etaEdges[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" \
% (dpix_ome, dpix_eta)
nHKLs = len(symHKLs_ix) - 1
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
# Compute the oscillation angles of all the symHKLs at once
oangs_pair = xfcapi.oscillAnglesOfHKLs(
symHKLs, 0., rMat, bMat, wavelength)
# Interleave the two produced oang solutions to simplify later processing
oangs = num.empty((len(symHKLs)*2, 3), dtype=oangs_pair[0].dtype)
oangs[0::2] = oangs_pair[0]
oangs[1::2] = oangs_pair[1]
# Map all of the angles at once
oangs[:, 1] = xf.mapAngle(oangs[:, 1])
oangs[:, 2] = xf.mapAngle(oangs[:, 2], omePeriod)
# Create a mask of the good ones
oangMask = num.logical_and(
~num.isnan(oangs[:, 0]),
num.logical_and(
xf.validateAngleRanges(oangs[:, 1], etaMin, etaMax),
xf.validateAngleRanges(oangs[:, 2], omeMin, omeMax)))
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
start, stop = symHKLs_ix[iHKL:iHKL+2]
start, stop = (2*start, 2*stop)
angList = oangs[start:stop]
angMask = oangMask[start:stop]
allAngs_m = angList[angMask, :]
if len(allAngs_m) > 0:
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack(
# [these_hkls, these_hkls]
# )[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = _meshgrid2d(
num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1)
)
i_sup = omeIndices[culledOmeIdx] + num.array(
[i_dil.flatten()], dtype=int
)
j_sup = etaIndices[culledEtaIdx] + num.array(
[j_dil.flatten()], dtype=int
)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(
num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max)
)
pixelVal = etaOmeMaps[iHKL][
i_sup[idx_mask], j_sup[idx_mask]
]
else:
pixelVal = etaOmeMaps[iHKL][
omeIndices[culledOmeIdx], etaIndices[culledEtaIdx]
]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
# if debug:
# print "hkl %d -->\t%d\t%d\t%d\t" % (
# iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh],
# culledHKLs[2, iTTh]
# ) \
# + "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) \
# + "eta index: %d,%d\tetaP: %g\n" % (
# culledEtaIdx, etaIndices[culledEtaIdx],
# r2d*culledEta[iTTh]
# ) \
# + "ome index: %d,%d\tomeP: %g\n" % (
# culledOmeIdx, omeIndices[culledOmeIdx],
# r2d*culledOme[iTTh]
# )
#
# close conditional on valid reflections
# close loop on signed reflections
# close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
def paintGridThis(quat):
"""
"""
# pull local vars from globals set in paintGrid
global symHKLs_MP, wavelength_MP
global omeMin_MP, omeMax_MP, omeTol_MP
global etaMin_MP, etaMax_MP, etaTol_MP
global omeIndices_MP, etaIndices_MP
global omeEdges_MP, etaEdges_MP
global hklList_MP, hklIDs_MP
global etaOmeMaps_MP
global bMat_MP
global threshold_MP
symHKLs = symHKLs_MP
wavelength = wavelength_MP
hklIDs = hklIDs_MP
hklList = hklList_MP
omeMin = omeMin_MP
omeMax = omeMax_MP
omeTol = omeTol_MP
omeIndices = omeIndices_MP
omeEdges = omeEdges_MP
etaMin = etaMin_MP
etaMax = etaMax_MP
etaTol = etaTol_MP
etaIndices = etaIndices_MP
etaEdges = etaEdges_MP
etaOmeMaps = etaOmeMaps_MP
bMat = bMat_MP
threshold = threshold_MP
# need this for proper index generation
omegas = [omeEdges[0] + (i+0.5)*(omeEdges[1] - omeEdges[0]) for i in range(len(omeEdges) - 1)]
etas = [etaEdges[0] + (i+0.5)*(etaEdges[1] - etaEdges[0]) for i in range(len(etaEdges) - 1)]
delOmeSign = num.sign(omegas[1] - omegas[0])
del_ome = abs(omegas[1] - omegas[0])
del_eta = abs(etas[1] - etas[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" % (dpix_ome, dpix_eta)
nHKLs = len(hklIDs)
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
# select and C-ify symmetric HKLs
these_hkls = num.array(symHKLs[hklIDs[iHKL]].T, dtype=float, order='C')
# oscillation angle arrays
oangs = xfcapi.oscillAnglesOfHKLs(these_hkls, 0., rMat, bMat, wavelength)
angList = num.vstack(oangs)
if not num.all(num.isnan(angList)):
angList[:, 1] = xf.mapAngle(angList[:, 1])
angList[:, 2] = xf.mapAngle(angList[:, 2])
if omeMin is None:
omeMin = [-num.pi, ]
omeMax = [ num.pi, ]
if etaMin is None:
etaMin = [-num.pi, ]
etaMax = [ num.pi, ]
angMask = num.logical_and(
xf.validateAngleRanges(angList[:, 1], etaMin, etaMax),
xf.validateAngleRanges(angList[:, 2], omeMin, omeMax))
allAngs_m = angList[angMask, :]
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack([these_hkls, these_hkls])[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = num.meshgrid(num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1))
i_sup = omeIndices[culledOmeIdx] + num.array([i_dil.flatten()], dtype=int)
j_sup = etaIndices[culledEtaIdx] + num.array([j_dil.flatten()], dtype=int)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max))
pixelVal = etaOmeMaps[iHKL][i_sup[idx_mask], j_sup[idx_mask]]
else:
pixelVal = etaOmeMaps[iHKL][omeIndices[culledOmeIdx], etaIndices[culledEtaIdx] ]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
pass
pass
# disabled # if debug:
# disabled # print "hkl %d -->\t%d\t%d\t%d\t" % (iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh], culledHKLs[2, iTTh]) + \
# disabled # "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) + \
# disabled # "eta index: %d,%d\tetaP: %g\n" % (culledEtaIdx, etaIndices[culledEtaIdx], r2d*culledEta[iTTh]) + \
# disabled # "ome index: %d,%d\tomeP: %g\n" % (culledOmeIdx, omeIndices[culledOmeIdx], r2d*culledOme[iTTh])
# disabled # pass
pass # close conditional on valid reflections
pass # close loop on signed reflections
pass # close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
def paintGridThis(quat):
"""
"""
# pull local vars from globals set in paintGrid
global symHKLs_MP, wavelength_MP
global omeMin_MP, omeMax_MP, omeTol_MP, omePeriod_MP
global etaMin_MP, etaMax_MP, etaTol_MP
global omeIndices_MP, etaIndices_MP
global omeEdges_MP, etaEdges_MP
global hklList_MP, hklIDs_MP
global etaOmeMaps_MP
global bMat_MP
global threshold_MP
symHKLs = symHKLs_MP
wavelength = wavelength_MP
hklIDs = hklIDs_MP
hklList = hklList_MP
omeMin = omeMin_MP
omeMax = omeMax_MP
omeTol = omeTol_MP
omePeriod = omePeriod_MP
omeIndices = omeIndices_MP
omeEdges = omeEdges_MP
etaMin = etaMin_MP
etaMax = etaMax_MP
etaTol = etaTol_MP
etaIndices = etaIndices_MP
etaEdges = etaEdges_MP
etaOmeMaps = etaOmeMaps_MP
bMat = bMat_MP
threshold = threshold_MP
# need this for proper index generation
omegas = [
omeEdges[0] + (i + 0.5) * (omeEdges[1] - omeEdges[0])
for i in range(len(omeEdges) - 1)
]
etas = [
etaEdges[0] + (i + 0.5) * (etaEdges[1] - etaEdges[0])
for i in range(len(etaEdges) - 1)
]
delOmeSign = num.sign(omegas[1] - omegas[0])
del_ome = abs(omegas[1] - omegas[0])
del_eta = abs(etas[1] - etas[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" % (dpix_ome,
dpix_eta)
nHKLs = len(hklIDs)
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
# select and C-ify symmetric HKLs
these_hkls = num.array(symHKLs[hklIDs[iHKL]].T, dtype=float, order='C')
# oscillation angle arrays
oangs = xfcapi.oscillAnglesOfHKLs(these_hkls, 0., rMat, bMat,
wavelength)
angList = num.vstack(oangs)
if not num.all(num.isnan(angList)):
idx = -num.isnan(angList[:, 0])
angList = angList[idx, :]
angList[:, 1] = xf.mapAngle(angList[:, 1])
angList[:, 2] = xf.mapAngle(angList[:, 2], omePeriod)
if omeMin is None:
omeMin = [
-num.pi,
]
omeMax = [
num.pi,
]
if etaMin is None:
etaMin = [
-num.pi,
]
etaMax = [
num.pi,
]
angMask = num.logical_and(
xf.validateAngleRanges(angList[:, 1], etaMin, etaMax),
xf.validateAngleRanges(angList[:, 2], omeMin, omeMax))
allAngs_m = angList[angMask, :]
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack([these_hkls, these_hkls])[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = num.meshgrid(
num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1))
i_sup = omeIndices[culledOmeIdx] + num.array(
[i_dil.flatten()], dtype=int)
j_sup = etaIndices[culledEtaIdx] + num.array(
[j_dil.flatten()], dtype=int)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(
num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max))
pixelVal = etaOmeMaps[iHKL][i_sup[idx_mask],
j_sup[idx_mask]]
else:
pixelVal = etaOmeMaps[iHKL][omeIndices[culledOmeIdx],
etaIndices[culledEtaIdx]]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
pass
pass
# disabled # if debug:
# disabled # print "hkl %d -->\t%d\t%d\t%d\t" % (iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh], culledHKLs[2, iTTh]) + \
# disabled # "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) + \
# disabled # "eta index: %d,%d\tetaP: %g\n" % (culledEtaIdx, etaIndices[culledEtaIdx], r2d*culledEta[iTTh]) + \
# disabled # "ome index: %d,%d\tomeP: %g\n" % (culledOmeIdx, omeIndices[culledOmeIdx], r2d*culledOme[iTTh])
# disabled # pass
pass # close conditional on valid reflections
pass # close loop on signed reflections
pass # close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
def calibrateDetectorFromSX(xyo_det,
hkls_idx,
bMat,
wavelength,
tiltAngles,
chi,
expMap_c,
tVec_d,
tVec_s,
tVec_c,
vInv=vInv_ref,
beamVec=bVec_ref,
etaVec=eta_ref,
distortion=(dFunc_ref, dParams_ref, dFlag_ref,
dScl_ref),
pFlag=pFlag_ref,
pScl=pScl_ref,
omePeriod=None,
factor=0.1,
xtol=sqrt_epsf,
ftol=sqrt_epsf):
"""
"""
if omePeriod is not None:
xyo_det[:, 2] = xf.mapAngle(xyo_det[:, 2], omePeriod)
# FIXME: this format for distortion needs to go away ASAP <JVB 2017-03-27>
dFunc = distortion[0]
dParams = distortion[1]
dFlag = distortion[2]
dScl = distortion[3]
"""
p = np.zeros(17)
p[0] = wavelength
p[1] = tiltAngles[0]
p[2] = tiltAngles[1]
p[3] = tiltAngles[2]
p[4] = tVec_d[0]
p[5] = tVec_d[1]
p[6] = tVec_d[2]
p[7] = chi
p[8] = tVec_s[0]
p[9] = tVec_s[1]
p[10] = tVec_s[2]
p[11] = expMap_c[0]
p[12] = expMap_c[1]
p[13] = expMap_c[2]
p[14] = tVec_c[0]
p[15] = tVec_c[1]
p[16] = tVec_c[2]
pFull = np.hstack([p, dParams])
"""
pFull = geomParamsToInput(wavelength, tiltAngles, chi, expMap_c, tVec_d,
tVec_s, tVec_c, dParams)
# TODO: check scaling <JVB 2017-03-27>
refineFlag = np.array(np.hstack([pFlag, dFlag]), dtyp=bool)
scl = np.hstack([pScl, dScl])
pFit = pFull[refineFlag]
fitArgs = (pFull, pFlag, dFunc, dFlag, xyo_det, hkls_idx, bMat, vInv,
beamVec, etaVec, omePeriod)
results = optimize.leastsq(objFuncSX,
pFit,
args=fitArgs,
diag=1. / scl[refineFlag].flatten(),
factor=factor,
xtol=xtol,
ftol=ftol)
pFit_opt = results[0]
retval = pFull
retval[refineFlag] = pFit_opt
return retval
def check_indexing_plots(cfg_filename, plot_trials=False, plot_from_grains=False):
cfg = config.open(cfg_filename)[0] # use first block, like indexing
working_dir = cfg.working_dir
analysis_dir = os.path.join(working_dir, cfg.analysis_name)
#instrument parameters
icfg = get_instrument_parameters(cfg)
chi = icfg['oscillation_stage']['chi']
# load maps that were used
oem = cPickle.load(
open(cfg.find_orientations.orientation_maps.file, 'r')
)
nmaps = len(oem.dataStore)
omeEdges = np.degrees(oem.omeEdges); nome = len(omeEdges) - 1
etaEdges = np.degrees(oem.etaEdges); neta = len(etaEdges) - 1
delta_ome = abs(omeEdges[1]-omeEdges[0])
full_ome_range = xf.angularDifference(omeEdges[0], omeEdges[-1]) == 0
full_eta_range = xf.angularDifference(etaEdges[0], etaEdges[-1]) == 0
# grab plane data and figure out IDs of map HKLS
pd = oem.planeData
gvids = [pd.hklDataList[i]['hklID'] for i in np.where(pd.exclusions == False)[0].tolist()]
# load orientations
quats = np.atleast_2d(np.loadtxt(os.path.join(working_dir, 'accepted_orientations.dat')))
if plot_trials:
scored_trials = np.load(os.path.join(working_dir, 'scored_orientations.dat'))
quats = scored_orientations[:4, scored_orientations[-1, :] >= cfg.find_orientations.clustering.completeness]
pass
expMaps = np.tile(2. * np.arccos(quats[:, 0]), (3, 1))*unitVector(quats[:, 1:].T)
##########################################
# SPECIAL CASE FOR FIT GRAINS #
##########################################
if plot_from_grains:
distortion = (GE_41RT, icfg['detector']['distortion']['parameters'])
#
grain_table = np.atleast_2d(np.loadtxt(os.path.join(analysis_dir, 'grains.out')))
ngrains = len(grain_table)
#
expMaps = grain_table[:, 3:6]
tVec_c = grain_table[:, 6:9]
vInv = grain_table[:, 6:12]
#
rMat_d = xf.makeDetectorRotMat(icfg['detector']['transform']['tilt_angles'])
tVec_d = np.vstack(icfg['detector']['transform']['t_vec_d'])
#
chi = icfg['oscillation_stage']['chi']
tVec_s = np.vstack(icfg['oscillation_stage']['t_vec_s'])
#
oes = np.zeros(oem.dataStore.shape)
for i_grn in range(ngrains):
spots_table = np.loadtxt(os.path.join(analysis_dir, 'spots_%05d.out' %i_grn))
idx_m = spots_table[:, 0] >= 0
for i_map in range(nmaps):
idx_g = spots_table[:, 1] == gvids[i_map]
idx = np.logical_and(idx_m, idx_g)
nrefl = sum(idx)
omes_fit = xf.mapAngle(spots_table[idx, 9], np.radians(cfg.find_orientations.omega.period), units='radians')
xy_det = spots_table[idx, -3:]
xy_det[:, 2] = np.zeros(nrefl)
rMat_s_array = xfcapi.makeOscillRotMatArray(chi, omes_fit)
# form in-plane vectors for detector points list in DETECTOR FRAME
P2_d = xy_det.T
# in LAB FRAME
P2_l = np.dot(rMat_d, P2_d) + tVec_d # point on detector
P0_l = np.hstack(
[tVec_s + np.dot(rMat_s_array[j], tVec_c[i_grn, :].reshape(3, 1)) for j in range(nrefl)]
) # origin of CRYSTAL FRAME
# diffraction unit vector components in LAB FRAME
dHat_l = unitVector(P2_l - P0_l)
P2_l = np.dot(rMat_d, xy_det.T) + tVec_d
# angles for reference frame
dHat_ref_l = unitVector(P2_l)
# append etas and omes
etas_fit = np.arctan2(dHat_ref_l[1, :], dHat_ref_l[0, :]).flatten()
# find indices, then truncate or wrap
i_ome = cellIndices(oem.omeEdges, omes_fit)
if full_ome_range:
i_ome[i_ome < 0] = np.mod(i_ome, nome) + 1
i_ome[i_ome >= nome] = np.mod(i_ome, nome)
else:
incl = np.logical_or(i_ome >= 0, i_ome < nome)
i_ome = i_ome[incl]
j_eta = cellIndices(oem.etaEdges, etas_fit)
if full_eta_range:
j_eta[j_eta < 0] = np.mod(j_eta, neta) + 1
j_eta[j_eta >= neta] = np.mod(j_eta, neta)
else:
incl = np.logical_or(j_eta >= 0, j_eta < neta)
j_eta = j_eta[incl]
#if np.max(i_ome) >= nome or np.min(i_ome) < 0 or np.max(j_eta) >= neta or np.min(j_eta) < 0:
# import pdb; pdb.set_trace()
# add to map
oes[i_map][i_ome, j_eta] = 1
pass
pass
# simulate quaternion points
if not plot_from_grains:
oes = simulateOmeEtaMaps(omeEdges, etaEdges, pd,
expMaps,
chi=chi,
etaTol=0.01, omeTol=0.01,
etaRanges=None, omeRanges=None,
bVec=xf.bVec_ref, eVec=xf.eta_ref, vInv=xf.vInv_ref)
# tick labling
omes = np.degrees(oem.omeEdges)
etas = np.degrees(oem.etaEdges)
num_ticks = 7
xmin = np.amin(etas); xmax = np.amax(etas)
dx = (xmax - xmin) / (num_ticks - 1.); dx1 = (len(etas) - 1) / (num_ticks - 1.)
xtlab = ["%.0f" % (xmin + i*dx) for i in range(num_ticks)]
xtloc = np.array([i*dx1 for i in range(num_ticks)]) - 0.5
ymin = np.amin(omes); ymax = np.amax(omes)
dy = (ymax - ymin) / (num_ticks - 1.); dy1 = (len(omes) - 1) / (num_ticks - 1.)
ytlab = ["%.0f" % (ymin + i*dy) for i in range(num_ticks)]
ytloc = np.array([i*dy1 for i in range(num_ticks)]) - 0.5
# Plot the three kernel density estimates
n_maps = len(oem.iHKLList)
fig_list =[plt.figure(num=i+1) for i in range(n_maps)]
ax_list = [fig_list[i].gca() for i in range(n_maps)]
for i_map in range(n_maps):
y, x = np.where(oes[i_map] > 0)
ax_list[i_map].hold(True)
ax_list[i_map].imshow(oem.dataStore[i_map] > 0.1, cmap=cm.bone)
ax_list[i_map].set_title(r'Map for $\{%d %d %d\}$' %tuple(pd.hkls[:, i_map]))
ax_list[i_map].set_xlabel(r'Azimuth channel, $\eta$; $\Delta\eta=%.3f$' %delta_ome)
ax_list[i_map].set_ylabel(r'Rotation channel, $\omega$; $\Delta\omega=%.3f$' %delta_ome)
ax_list[i_map].plot(x, y, 'c+')
ax_list[i_map].xaxis.set_ticks(xtloc)
ax_list[i_map].xaxis.set_ticklabels(xtlab)
ax_list[i_map].yaxis.set_ticks(ytloc)
ax_list[i_map].yaxis.set_ticklabels(ytlab)
ax_list[i_map].axis('tight')
plt.show()
return fig_list, oes
def check_indexing_plots(cfg_filename,
plot_trials=False,
plot_from_grains=False):
cfg = config.open(cfg_filename)[0] # use first block, like indexing
working_dir = cfg.working_dir
analysis_dir = os.path.join(working_dir, cfg.analysis_name)
#instrument parameters
icfg = get_instrument_parameters(cfg)
chi = icfg['oscillation_stage']['chi']
# load maps that were used
oem = cPickle.load(open(cfg.find_orientations.orientation_maps.file, 'r'))
nmaps = len(oem.dataStore)
omeEdges = np.degrees(oem.omeEdges)
nome = len(omeEdges) - 1
etaEdges = np.degrees(oem.etaEdges)
neta = len(etaEdges) - 1
delta_ome = abs(omeEdges[1] - omeEdges[0])
full_ome_range = xf.angularDifference(omeEdges[0], omeEdges[-1]) == 0
full_eta_range = xf.angularDifference(etaEdges[0], etaEdges[-1]) == 0
# grab plane data and figure out IDs of map HKLS
pd = oem.planeData
gvids = [
pd.hklDataList[i]['hklID']
for i in np.where(pd.exclusions == False)[0].tolist()
]
# load orientations
quats = np.atleast_2d(
np.loadtxt(os.path.join(working_dir, 'accepted_orientations.dat')))
if plot_trials:
scored_trials = np.load(
os.path.join(working_dir, 'scored_orientations.dat'))
quats = scored_orientations[:4, scored_orientations[
-1, :] >= cfg.find_orientations.clustering.completeness]
pass
expMaps = np.tile(2. * np.arccos(quats[:, 0]),
(3, 1)) * unitVector(quats[:, 1:].T)
##########################################
# SPECIAL CASE FOR FIT GRAINS #
##########################################
if plot_from_grains:
distortion = (GE_41RT, icfg['detector']['distortion']['parameters'])
#
grain_table = np.atleast_2d(
np.loadtxt(os.path.join(analysis_dir, 'grains.out')))
ngrains = len(grain_table)
#
expMaps = grain_table[:, 3:6]
tVec_c = grain_table[:, 6:9]
vInv = grain_table[:, 6:12]
#
rMat_d = xf.makeDetectorRotMat(
icfg['detector']['transform']['tilt_angles'])
tVec_d = np.vstack(icfg['detector']['transform']['t_vec_d'])
#
chi = icfg['oscillation_stage']['chi']
tVec_s = np.vstack(icfg['oscillation_stage']['t_vec_s'])
#
oes = np.zeros(oem.dataStore.shape)
for i_grn in range(ngrains):
spots_table = np.loadtxt(
os.path.join(analysis_dir, 'spots_%05d.out' % i_grn))
idx_m = spots_table[:, 0] >= 0
for i_map in range(nmaps):
idx_g = spots_table[:, 1] == gvids[i_map]
idx = np.logical_and(idx_m, idx_g)
nrefl = sum(idx)
omes_fit = xf.mapAngle(spots_table[idx, 9],
np.radians(
cfg.find_orientations.omega.period),
units='radians')
xy_det = spots_table[idx, -3:]
xy_det[:, 2] = np.zeros(nrefl)
rMat_s_array = xfcapi.makeOscillRotMatArray(chi, omes_fit)
# form in-plane vectors for detector points list in DETECTOR FRAME
P2_d = xy_det.T
# in LAB FRAME
P2_l = np.dot(rMat_d, P2_d) + tVec_d # point on detector
P0_l = np.hstack([
tVec_s +
np.dot(rMat_s_array[j], tVec_c[i_grn, :].reshape(3, 1))
for j in range(nrefl)
]) # origin of CRYSTAL FRAME
# diffraction unit vector components in LAB FRAME
dHat_l = unitVector(P2_l - P0_l)
P2_l = np.dot(rMat_d, xy_det.T) + tVec_d
# angles for reference frame
dHat_ref_l = unitVector(P2_l)
# append etas and omes
etas_fit = np.arctan2(dHat_ref_l[1, :],
dHat_ref_l[0, :]).flatten()
# find indices, then truncate or wrap
i_ome = cellIndices(oem.omeEdges, omes_fit)
if full_ome_range:
i_ome[i_ome < 0] = np.mod(i_ome, nome) + 1
i_ome[i_ome >= nome] = np.mod(i_ome, nome)
else:
incl = np.logical_or(i_ome >= 0, i_ome < nome)
i_ome = i_ome[incl]
j_eta = cellIndices(oem.etaEdges, etas_fit)
if full_eta_range:
j_eta[j_eta < 0] = np.mod(j_eta, neta) + 1
j_eta[j_eta >= neta] = np.mod(j_eta, neta)
else:
incl = np.logical_or(j_eta >= 0, j_eta < neta)
j_eta = j_eta[incl]
#if np.max(i_ome) >= nome or np.min(i_ome) < 0 or np.max(j_eta) >= neta or np.min(j_eta) < 0:
# import pdb; pdb.set_trace()
# add to map
oes[i_map][i_ome, j_eta] = 1
pass
pass
# simulate quaternion points
if not plot_from_grains:
oes = simulateOmeEtaMaps(omeEdges,
etaEdges,
pd,
expMaps,
chi=chi,
etaTol=0.01,
omeTol=0.01,
etaRanges=None,
omeRanges=None,
bVec=xf.bVec_ref,
eVec=xf.eta_ref,
vInv=xf.vInv_ref)
# tick labling
omes = np.degrees(oem.omeEdges)
etas = np.degrees(oem.etaEdges)
num_ticks = 7
xmin = np.amin(etas)
xmax = np.amax(etas)
dx = (xmax - xmin) / (num_ticks - 1.)
dx1 = (len(etas) - 1) / (num_ticks - 1.)
xtlab = ["%.0f" % (xmin + i * dx) for i in range(num_ticks)]
xtloc = np.array([i * dx1 for i in range(num_ticks)]) - 0.5
ymin = np.amin(omes)
ymax = np.amax(omes)
dy = (ymax - ymin) / (num_ticks - 1.)
dy1 = (len(omes) - 1) / (num_ticks - 1.)
ytlab = ["%.0f" % (ymin + i * dy) for i in range(num_ticks)]
ytloc = np.array([i * dy1 for i in range(num_ticks)]) - 0.5
# Plot the three kernel density estimates
n_maps = len(oem.iHKLList)
fig_list = [plt.figure(num=i + 1) for i in range(n_maps)]
ax_list = [fig_list[i].gca() for i in range(n_maps)]
for i_map in range(n_maps):
y, x = np.where(oes[i_map] > 0)
ax_list[i_map].hold(True)
ax_list[i_map].imshow(oem.dataStore[i_map] > 0.1, cmap=cm.bone)
ax_list[i_map].set_title(r'Map for $\{%d %d %d\}$' %
tuple(pd.hkls[:, i_map]))
ax_list[i_map].set_xlabel(
r'Azimuth channel, $\eta$; $\Delta\eta=%.3f$' % delta_ome)
ax_list[i_map].set_ylabel(
r'Rotation channel, $\omega$; $\Delta\omega=%.3f$' % delta_ome)
ax_list[i_map].plot(x, y, 'c+')
ax_list[i_map].xaxis.set_ticks(xtloc)
ax_list[i_map].xaxis.set_ticklabels(xtlab)
ax_list[i_map].yaxis.set_ticks(ytloc)
ax_list[i_map].yaxis.set_ticklabels(ytlab)
ax_list[i_map].axis('tight')
plt.show()
return fig_list, oes