def simulate_laue_pattern(self,
crystal_data,
minEnergy=5.,
maxEnergy=35.,
rmat_s=None,
tvec_s=None,
grain_params=None,
beam_vec=None):
"""
"""
if isinstance(crystal_data, PlaneData):
plane_data = crystal_data
# grab the expanded list of hkls from plane_data
hkls = np.hstack(plane_data.getSymHKLs())
# and the unit plane normals (G-vectors) in CRYSTAL FRAME
gvec_c = np.dot(plane_data.latVecOps['B'], hkls)
elif len(crystal_data) == 2:
# !!! should clean this up
hkls = np.array(crystal_data[0])
bmat = crystal_data[1]
gvec_c = np.dot(bmat, hkls)
else:
raise (RuntimeError, 'argument list not understood')
nhkls_tot = hkls.shape[1]
# parse energy ranges
# TODO: allow for spectrum parsing
multipleEnergyRanges = False
if hasattr(maxEnergy, '__len__'):
assert len(maxEnergy) == len(minEnergy), \
'energy cutoff ranges must have the same length'
multipleEnergyRanges = True
lmin = []
lmax = []
for i in range(len(maxEnergy)):
lmin.append(ct.keVToAngstrom(maxEnergy[i]))
lmax.append(ct.keVToAngstrom(minEnergy[i]))
else:
lmin = ct.keVToAngstrom(maxEnergy)
lmax = ct.keVToAngstrom(minEnergy)
# parse grain parameters kwarg
if grain_params is None:
grain_params = np.atleast_2d(
np.hstack([np.zeros(6), ct.identity_6x1]))
n_grains = len(grain_params)
# sample rotation
if rmat_s is None:
rmat_s = ct.identity_3x3
# dummy translation vector... make input
if tvec_s is None:
tvec_s = ct.zeros_3
# beam vector
if beam_vec is None:
beam_vec = ct.beam_vec
# =========================================================================
# LOOP OVER GRAINS
# =========================================================================
# pre-allocate output arrays
xy_det = np.nan * np.ones((n_grains, nhkls_tot, 2))
hkls_in = np.nan * np.ones((n_grains, 3, nhkls_tot))
angles = np.nan * np.ones((n_grains, nhkls_tot, 2))
dspacing = np.nan * np.ones((n_grains, nhkls_tot))
energy = np.nan * np.ones((n_grains, nhkls_tot))
for iG, gp in enumerate(grain_params):
rmat_c = makeRotMatOfExpMap(gp[:3])
tvec_c = gp[3:6].reshape(3, 1)
vInv_s = mutil.vecMVToSymm(gp[6:].reshape(6, 1))
# stretch them: V^(-1) * R * Gc
gvec_s_str = np.dot(vInv_s, np.dot(rmat_c, gvec_c))
ghat_c_str = mutil.unitVector(np.dot(rmat_c.T, gvec_s_str))
# project
dpts = gvecToDetectorXY(ghat_c_str.T,
self.rmat,
rmat_s,
rmat_c,
self.tvec,
tvec_s,
tvec_c,
beamVec=beam_vec)
# check intersections with detector plane
canIntersect = ~np.isnan(dpts[:, 0])
npts_in = sum(canIntersect)
if np.any(canIntersect):
dpts = dpts[canIntersect, :].reshape(npts_in, 2)
dhkl = hkls[:, canIntersect].reshape(3, npts_in)
# back to angles
tth_eta, gvec_l = detectorXYToGvec(dpts,
self.rmat,
rmat_s,
self.tvec,
tvec_s,
tvec_c,
beamVec=beam_vec)
tth_eta = np.vstack(tth_eta).T
# warp measured points
if self.distortion is not None:
if len(self.distortion) == 2:
dpts = self.distortion[0](dpts,
self.distortion[1],
invert=True)
else:
raise (RuntimeError,
"something is wrong with the distortion")
# plane spacings and energies
dsp = 1. / rowNorm(gvec_s_str[:, canIntersect].T)
wlen = 2 * dsp * np.sin(0.5 * tth_eta[:, 0])
# clip to detector panel
_, on_panel = self.clip_to_panel(dpts, buffer_edges=True)
if multipleEnergyRanges:
validEnergy = np.zeros(len(wlen), dtype=bool)
for i in range(len(lmin)):
in_energy_range = np.logical_and(
wlen >= lmin[i], wlen <= lmax[i])
validEnergy = validEnergy | in_energy_range
pass
else:
validEnergy = np.logical_and(wlen >= lmin, wlen <= lmax)
pass
# index for valid reflections
keepers = np.where(np.logical_and(on_panel, validEnergy))[0]
# assign output arrays
xy_det[iG][keepers, :] = dpts[keepers, :]
hkls_in[iG][:, keepers] = dhkl[:, keepers]
angles[iG][keepers, :] = tth_eta[keepers, :]
dspacing[iG, keepers] = dsp[keepers]
energy[iG, keepers] = ct.keVToAngstrom(wlen[keepers])
pass # close conditional on valids
pass # close loop on grains
return xy_det, hkls_in, angles, dspacing, energy
def calibrate_instrument_from_sx(instr,
grain_params,
bmat,
xyo_det,
hkls_idx,
param_flags=None,
dparam_flags=None,
ome_period=None,
xtol=cnst.sqrt_epsf,
ftol=cnst.sqrt_epsf,
factor=10.,
sim_only=False,
use_robust_lsq=False):
"""
arguments xyo_det, hkls_idx are DICTs over panels
!!!
distortion is still hosed...
Currently a dict of detector keys with
distortion[key] = [d_func, d_params, d_flags]
"""
pnames = [
'{:>24s}'.format('wavelength'),
'{:>24s}'.format('chi'),
'{:>24s}'.format('tvec_s[0]'),
'{:>24s}'.format('tvec_s[1]'),
'{:>24s}'.format('tvec_s[2]'),
'{:>24s}'.format('expmap_c[0]'),
'{:>24s}'.format('expmap_c[0]'),
'{:>24s}'.format('expmap_c[0]'),
'{:>24s}'.format('tvec_c[0]'),
'{:>24s}'.format('tvec_c[1]'),
'{:>24s}'.format('tvec_c[2]'),
]
for det_key, panel in instr.detectors.iteritems():
pnames += [
'{:>24s}'.format('%s tilt[0]' % det_key),
'{:>24s}'.format('%s tilt[1]' % det_key),
'{:>24s}'.format('%s tilt[2]' % det_key),
'{:>24s}'.format('%s tvec[0]' % det_key),
'{:>24s}'.format('%s tvec[1]' % det_key),
'{:>24s}'.format('%s tvec[2]' % det_key),
]
# now add distortion if
for det_key, panel in instr.detectors.iteritems():
if panel.distortion is not None:
for j in range(len(panel.distortion[1])):
pnames.append('{:>24s}'.format('%s dparam[%d]' % (det_key, j)))
# reset parameter flags for instrument as specified
if param_flags is None:
param_flags = instr.param_flags
else:
# will throw an AssertionError if wrong length
instr.param_flags = param_flags
det_keys = instr.detectors.keys()
# re-map omegas if need be
if ome_period is not None:
for det_key in det_keys:
xyo_det[det_key][:, 2] = xfcapi.mapAngle(xyo_det[det_key][:, 2],
ome_period)
# grain parameters
expmap_c = grain_params[:3]
tvec_c = grain_params[3:6]
vinv_s = grain_params[6:]
plist_full = instr.calibration_params(expmap_c, tvec_c)
dfuncs = {}
ndparams = {}
dparam_flags = []
for det_key, panel in instr.detectors.iteritems():
if panel.distortion is not None:
dfuncs[det_key] = panel.distortion[0]
# ititialize to all False...
ndparams[det_key] = len(panel.distortion[1])
else:
dfuncs[det_key] = None
ndparams[det_key] = 0
dparam_flags.append(np.zeros(ndparams[det_key], dtype=bool))
dparam_flags = np.hstack(dparam_flags)
refine_flags = np.hstack([param_flags, dparam_flags])
plist_fit = plist_full[refine_flags]
fit_args = (plist_full, param_flags, dfuncs, dparam_flags, ndparams, instr,
xyo_det, hkls_idx, bmat, vinv_s, ome_period, instr.beam_vector,
instr.eta_vector)
if sim_only:
return sxcal_obj_func(plist_fit,
plist_full,
param_flags,
dfuncs,
dparam_flags,
ndparams,
instr,
xyo_det,
hkls_idx,
bmat,
vinv_s,
ome_period,
instr.beam_vector,
instr.eta_vector,
sim_only=True)
else:
print("Set up to refine:")
for i in np.where(refine_flags)[0]:
print("\t%s = %1.7e" % (pnames[i], plist_full[i]))
# run optimization
if use_robust_lsq:
result = least_squares(sxcal_obj_func,
plist_fit,
args=fit_args,
xtol=xtol,
ftol=ftol,
loss='soft_l1',
method='trf')
x = result.x
resd = result.fun
mesg = result.message
ierr = result.status
else:
# do least squares problem
x, cov_x, infodict, mesg, ierr = leastsq(sxcal_obj_func,
plist_fit,
args=fit_args,
factor=factor,
xtol=xtol,
ftol=ftol,
full_output=1)
resd = infodict['fvec']
if ierr not in [1, 2, 3, 4]:
raise RuntimeError("solution not found: ierr = %d" % ierr)
else:
print("INFO: optimization fininshed successfully with ierr=%d" %
ierr)
print("INFO: %s" % mesg)
# ??? output message handling?
fit_params = plist_full
fit_params[refine_flags] = x
# run simulation with optimized results
sim_final = sxcal_obj_func(x,
plist_full,
param_flags,
dfuncs,
dparam_flags,
ndparams,
instr,
xyo_det,
hkls_idx,
bmat,
vinv_s,
ome_period,
instr.beam_vector,
instr.eta_vector,
sim_only=True)
# ??? reset instrument here?
instr.beam_energy = cnst.keVToAngstrom(fit_params[0])
instr.chi = fit_params[1]
instr.tvec = fit_params[2:5]
ii = 11
for det_key, panel in instr.detectors.iteritems():
panel.tilt = fit_params[ii:ii + 3]
panel.tvec = fit_params[ii + 3:ii + 6]
ii += 6
# !!! use jj to do distortion...
if panel.distortion is not None:
pass
pass
return fit_params, resd, sim_final
def simulate_rotation_series(self,
plane_data,
grain_param_list,
eta_ranges=[
(-np.pi, np.pi),
],
ome_ranges=[
(-np.pi, np.pi),
],
ome_period=(-np.pi, np.pi),
chi=0.,
tVec_s=ct.zeros_3,
wavelength=None):
"""
"""
# grab B-matrix from plane data
bMat = plane_data.latVecOps['B']
# reconcile wavelength
# * added sanity check on exclusions here; possible to
# * make some reflections invalid (NaN)
if wavelength is None:
wavelength = plane_data.wavelength
else:
if plane_data.wavelength != wavelength:
plane_data.wavelength = ct.keVToAngstrom(wavelength)
assert not np.any(np.isnan(plane_data.getTTh())),\
"plane data exclusions incompatible with wavelength"
# vstacked G-vector id, h, k, l
full_hkls = xrdutil._fetch_hkls_from_planedata(plane_data)
""" LOOP OVER GRAINS """
valid_ids = []
valid_hkls = []
valid_angs = []
valid_xys = []
ang_pixel_size = []
for gparm in grain_param_list:
# make useful parameters
rMat_c = makeRotMatOfExpMap(gparm[:3])
tVec_c = gparm[3:6]
vInv_s = gparm[6:]
# All possible bragg conditions as vstacked [tth, eta, ome]
# for each omega solution
angList = np.vstack(
oscillAnglesOfHKLs(
full_hkls[:, 1:],
chi,
rMat_c,
bMat,
wavelength,
vInv=vInv_s,
))
# filter by eta and omega ranges
# ??? get eta range from detector?
allAngs, allHKLs = xrdutil._filter_hkls_eta_ome(
full_hkls, angList, eta_ranges, ome_ranges)
allAngs[:, 2] = mapAngle(allAngs[:, 2], ome_period)
# find points that fall on the panel
det_xy, rMat_s = xrdutil._project_on_detector_plane(
allAngs, self.rmat, rMat_c, chi, self.tvec, tVec_c, tVec_s,
self.distortion)
xys_p, on_panel = self.clip_to_panel(det_xy)
valid_xys.append(xys_p)
# grab hkls and gvec ids for this panel
valid_hkls.append(allHKLs[on_panel, 1:])
valid_ids.append(allHKLs[on_panel, 0])
# reflection angles (voxel centers) and pixel size in (tth, eta)
valid_angs.append(allAngs[on_panel, :])
ang_pixel_size.append(self.angularPixelSize(xys_p))
return valid_ids, valid_hkls, valid_angs, valid_xys, ang_pixel_size
def wavelength(self):
return constants.keVToAngstrom(self.energy)
def wavelength(self, x):
"""
in angstrom
"""
self._energy = constants.keVToAngstrom(x)
def mockup_experiment():
# user options
# each grain is provided in the form of a quaternion.
# The following array contains the quaternions for the array. Note that the
# quaternions are in the columns, with the first row (row 0) being the real
# part w. We assume that we are dealing with unit quaternions
quats = np.array([[0.91836393, 0.90869942], [0.33952917, 0.18348350],
[0.17216207, 0.10095837], [0.10811041, 0.36111851]])
n_grains = quats.shape[-1] # last dimension provides the number of grains
phis = 2. * np.arccos(
quats[0, :]) # phis are the angles for the quaternion
# ns contains the rotation axis as an unit vector
ns = hexrd.matrixutil.unitVector(quats[1:, :])
exp_maps = np.array([phis[i] * ns[:, i] for i in range(n_grains)])
rMat_c = rotations.rotMatOfQuat(quats)
cvec = np.arange(-25, 26)
X, Y, Z = np.meshgrid(cvec, cvec, cvec)
crd0 = 1e-3 * np.vstack([X.flatten(), Y.flatten(), Z.flatten()]).T
crd1 = crd0 + np.r_[0.100, 0.100, 0]
crds = np.array([crd0, crd1])
# make grain parameters
grain_params = []
for i in range(n_grains):
for j in range(len(crd0)):
grain_params.append(
np.hstack([exp_maps[i, :], crds[i][j, :], vInv_ref]))
# scan range and period
ome_period = (0, 2 * np.pi)
ome_range = [
ome_period,
]
ome_step = np.radians(1.)
nframes = 0
for i in range(len(ome_range)):
nframes += int((ome_range[i][1] - ome_range[i][0]) / ome_step)
ome_edges = np.arange(nframes + 1) * ome_step
# instrument
with open('./retiga.yml', 'r') as fildes:
instr = instrument.HEDMInstrument(yaml.safe_load(fildes))
panel = next(iter(instr.detectors.values())) # !!! there is only 1
# tranform paramters
# Sample
chi = instr.chi
tVec_s = instr.tvec
# Detector
rMat_d = panel.rmat
tilt_angles_xyzp = np.asarray(rotations.angles_from_rmat_xyz(rMat_d))
tVec_d = panel.tvec
# pixels
row_ps = panel.pixel_size_row
col_ps = panel.pixel_size_col
pixel_size = (row_ps, col_ps)
nrows = panel.rows
ncols = panel.cols
# panel dimensions
panel_dims = [tuple(panel.corner_ll), tuple(panel.corner_ur)]
x_col_edges = panel.col_edge_vec
y_row_edges = panel.row_edge_vec
rx, ry = np.meshgrid(x_col_edges, y_row_edges)
max_pixel_tth = instrument.max_tth(instr)
detector_params = np.hstack([tilt_angles_xyzp, tVec_d, chi, tVec_s])
distortion = panel.distortion # !!! must be None for now
# a different parametrization for the sensor
# (makes for faster quantization)
base = np.array([x_col_edges[0], y_row_edges[0], ome_edges[0]])
deltas = np.array([
x_col_edges[1] - x_col_edges[0], y_row_edges[1] - y_row_edges[0],
ome_edges[1] - ome_edges[0]
])
inv_deltas = 1.0 / deltas
clip_vals = np.array([ncols, nrows])
# dilation
max_diameter = np.sqrt(3) * 0.005
row_dilation = int(np.ceil(0.5 * max_diameter / row_ps))
col_dilation = int(np.ceil(0.5 * max_diameter / col_ps))
# crystallography data
beam_energy = valunits.valWUnit("beam_energy", "energy", instr.beam_energy,
"keV")
beam_wavelength = constants.keVToAngstrom(beam_energy.getVal('keV'))
dmin = valunits.valWUnit(
"dmin", "length", 0.5 * beam_wavelength / np.sin(0.5 * max_pixel_tth),
"angstrom")
gold = material.Material()
gold.latticeParameters = [4.0782]
gold.dmin = dmin
gold.beamEnergy = beam_energy
gold.planeData.exclusions = None
gold.planeData.tThMax = max_pixel_tth # note this comes detector
ns = argparse.Namespace()
# grains related information
ns.n_grains = n_grains # this can be derived from other values...
ns.rMat_c = rMat_c # n_grains rotation matrices (one per grain)
ns.exp_maps = exp_maps # n_grains exp_maps (one per grain)
ns.plane_data = gold.planeData
ns.detector_params = detector_params
ns.pixel_size = pixel_size
ns.ome_range = ome_range
ns.ome_period = ome_period
ns.x_col_edges = x_col_edges
ns.y_row_edges = y_row_edges
ns.ome_edges = ome_edges
ns.ncols = ncols
ns.nrows = nrows
ns.nframes = nframes # used only in simulate...
ns.rMat_d = rMat_d
ns.tVec_d = tVec_d
ns.chi = chi # note this is used to compute S... why is it needed?
ns.tVec_s = tVec_s
ns.rMat_c = rMat_c
ns.row_dilation = row_dilation
ns.col_dilation = col_dilation
ns.distortion = distortion
ns.panel_dims = panel_dims # used only in simulate...
ns.base = base
ns.inv_deltas = inv_deltas
ns.clip_vals = clip_vals
return grain_params, ns
from enum import Enum import numpy as np from hexrd import constants # Wavelength to kilo electron volt conversion WAVELENGTH_TO_KEV = constants.keVToAngstrom(1.) KEV_TO_WAVELENGTH = constants.keVToAngstrom(1.) DEFAULT_CMAP = 'plasma' UI_DARK_INDEX_MEDIAN = 0 UI_DARK_INDEX_EMPTY_FRAMES = 1 UI_DARK_INDEX_AVERAGE = 2 UI_DARK_INDEX_MAXIMUM = 3 UI_DARK_INDEX_FILE = 4 UI_DARK_INDEX_NONE = 5 UI_TRANS_INDEX_NONE = 0 UI_TRANS_INDEX_FLIP_VERTICALLY = 1 UI_TRANS_INDEX_FLIP_HORIZONTALLY = 2 UI_TRANS_INDEX_TRANSPOSE = 3 UI_TRANS_INDEX_ROTATE_90 = 4 UI_TRANS_INDEX_ROTATE_180 = 5 UI_TRANS_INDEX_ROTATE_270 = 6 UI_AGG_INDEX_NONE = 0 UI_AGG_INDEX_MAXIMUM = 1 UI_AGG_INDEX_MEDIAN = 2 UI_AGG_INDEX_AVERAGE = 3
def wavelength(self):
return constants.keVToAngstrom(self.energy)
def wavelength(self, x):
"""
in angstrom
"""
self._energy = constants.keVToAngstrom(x)
instr = instrument.HEDMInstrument(instr_cfg)
data_path = './'
img_series_root = 'ge_scan_114'
img_series = imageseries.open(
os.path.join(
img_series_root + '-fcache-dir', img_series_root + '-fcache.yml'
)
, 'frame-cache')
nframes = 240
average_frame = imageseries.stats.average(img_series)
#%%
wlen = constants.keVToAngstrom(instr_cfg['beam']['energy'])
matl = make_matl('LSHR', 225, [3.5905,])
pd = matl.planeData
pd.wavelength = instr_cfg['beam']['energy'] # takes keV
pd.exclusions = np.zeros_like(pd.exclusions, dtype=bool)
set_by_tth_max = False
if set_by_tth_max:
pd.tThMax = np.radians(6.75)
tth_del = np.radians(0.75)
tth_avg = np.average(pd.getTTh())
tth_lo = pd.getTTh()[0] - tth_del
tth_hi = pd.getTTh()[-1] + tth_del
else:
def simulate_laue_pattern(self, crystal_data,
minEnergy=5., maxEnergy=35.,
rmat_s=None, tvec_s=None,
grain_params=None,
beam_vec=None):
"""
"""
if isinstance(crystal_data, PlaneData):
plane_data = crystal_data
# grab the expanded list of hkls from plane_data
hkls = np.hstack(plane_data.getSymHKLs())
# and the unit plane normals (G-vectors) in CRYSTAL FRAME
gvec_c = np.dot(plane_data.latVecOps['B'], hkls)
elif len(crystal_data) == 2:
# !!! should clean this up
hkls = np.array(crystal_data[0])
bmat = crystal_data[1]
gvec_c = np.dot(bmat, hkls)
else:
raise(RuntimeError, 'argument list not understood')
nhkls_tot = hkls.shape[1]
# parse energy ranges
# TODO: allow for spectrum parsing
multipleEnergyRanges = False
if hasattr(maxEnergy, '__len__'):
assert len(maxEnergy) == len(minEnergy), \
'energy cutoff ranges must have the same length'
multipleEnergyRanges = True
lmin = []
lmax = []
for i in range(len(maxEnergy)):
lmin.append(ct.keVToAngstrom(maxEnergy[i]))
lmax.append(ct.keVToAngstrom(minEnergy[i]))
else:
lmin = ct.keVToAngstrom(maxEnergy)
lmax = ct.keVToAngstrom(minEnergy)
# parse grain parameters kwarg
if grain_params is None:
grain_params = np.atleast_2d(
np.hstack([np.zeros(6), ct.identity_6x1])
)
n_grains = len(grain_params)
# sample rotation
if rmat_s is None:
rmat_s = ct.identity_3x3
# dummy translation vector... make input
if tvec_s is None:
tvec_s = ct.zeros_3
# beam vector
if beam_vec is None:
beam_vec = ct.beam_vec
# =========================================================================
# LOOP OVER GRAINS
# =========================================================================
# pre-allocate output arrays
xy_det = np.nan*np.ones((n_grains, nhkls_tot, 2))
hkls_in = np.nan*np.ones((n_grains, 3, nhkls_tot))
angles = np.nan*np.ones((n_grains, nhkls_tot, 2))
dspacing = np.nan*np.ones((n_grains, nhkls_tot))
energy = np.nan*np.ones((n_grains, nhkls_tot))
for iG, gp in enumerate(grain_params):
rmat_c = makeRotMatOfExpMap(gp[:3])
tvec_c = gp[3:6].reshape(3, 1)
vInv_s = mutil.vecMVToSymm(gp[6:].reshape(6, 1))
# stretch them: V^(-1) * R * Gc
gvec_s_str = np.dot(vInv_s, np.dot(rmat_c, gvec_c))
ghat_c_str = mutil.unitVector(np.dot(rmat_c.T, gvec_s_str))
# project
dpts = gvecToDetectorXY(ghat_c_str.T,
self.rmat, rmat_s, rmat_c,
self.tvec, tvec_s, tvec_c,
beamVec=beam_vec)
# check intersections with detector plane
canIntersect = ~np.isnan(dpts[:, 0])
npts_in = sum(canIntersect)
if np.any(canIntersect):
dpts = dpts[canIntersect, :].reshape(npts_in, 2)
dhkl = hkls[:, canIntersect].reshape(3, npts_in)
# back to angles
tth_eta, gvec_l = detectorXYToGvec(
dpts,
self.rmat, rmat_s,
self.tvec, tvec_s, tvec_c,
beamVec=beam_vec)
tth_eta = np.vstack(tth_eta).T
# warp measured points
if self.distortion is not None:
if len(self.distortion) == 2:
dpts = self.distortion[0](
dpts, self.distortion[1],
invert=True)
else:
raise(RuntimeError,
"something is wrong with the distortion")
# plane spacings and energies
dsp = 1. / rowNorm(gvec_s_str[:, canIntersect].T)
wlen = 2*dsp*np.sin(0.5*tth_eta[:, 0])
# clip to detector panel
_, on_panel = self.clip_to_panel(dpts, buffer_edges=True)
if multipleEnergyRanges:
validEnergy = np.zeros(len(wlen), dtype=bool)
for i in range(len(lmin)):
in_energy_range = np.logical_and(
wlen >= lmin[i],
wlen <= lmax[i])
validEnergy = validEnergy | in_energy_range
pass
else:
validEnergy = np.logical_and(wlen >= lmin, wlen <= lmax)
pass
# index for valid reflections
keepers = np.where(np.logical_and(on_panel, validEnergy))[0]
# assign output arrays
xy_det[iG][keepers, :] = dpts[keepers, :]
hkls_in[iG][:, keepers] = dhkl[:, keepers]
angles[iG][keepers, :] = tth_eta[keepers, :]
dspacing[iG, keepers] = dsp[keepers]
energy[iG, keepers] = ct.keVToAngstrom(wlen[keepers])
pass # close conditional on valids
pass # close loop on grains
return xy_det, hkls_in, angles, dspacing, energy
def simulate_rotation_series(self, plane_data, grain_param_list,
eta_ranges=[(-np.pi, np.pi), ],
ome_ranges=[(-np.pi, np.pi), ],
ome_period=(-np.pi, np.pi),
chi=0., tVec_s=ct.zeros_3,
wavelength=None):
"""
"""
# grab B-matrix from plane data
bMat = plane_data.latVecOps['B']
# reconcile wavelength
# * added sanity check on exclusions here; possible to
# * make some reflections invalid (NaN)
if wavelength is None:
wavelength = plane_data.wavelength
else:
if plane_data.wavelength != wavelength:
plane_data.wavelength = ct.keVToAngstrom(wavelength)
assert not np.any(np.isnan(plane_data.getTTh())),\
"plane data exclusions incompatible with wavelength"
# vstacked G-vector id, h, k, l
full_hkls = xrdutil._fetch_hkls_from_planedata(plane_data)
""" LOOP OVER GRAINS """
valid_ids = []
valid_hkls = []
valid_angs = []
valid_xys = []
ang_pixel_size = []
for gparm in grain_param_list:
# make useful parameters
rMat_c = makeRotMatOfExpMap(gparm[:3])
tVec_c = gparm[3:6]
vInv_s = gparm[6:]
# All possible bragg conditions as vstacked [tth, eta, ome]
# for each omega solution
angList = np.vstack(
oscillAnglesOfHKLs(
full_hkls[:, 1:], chi,
rMat_c, bMat, wavelength,
vInv=vInv_s,
)
)
# filter by eta and omega ranges
# ??? get eta range from detector?
allAngs, allHKLs = xrdutil._filter_hkls_eta_ome(
full_hkls, angList, eta_ranges, ome_ranges
)
allAngs[:, 2] = mapAngle(allAngs[:, 2], ome_period)
# find points that fall on the panel
det_xy, rMat_s = xrdutil._project_on_detector_plane(
allAngs,
self.rmat, rMat_c, chi,
self.tvec, tVec_c, tVec_s,
self.distortion)
xys_p, on_panel = self.clip_to_panel(det_xy)
valid_xys.append(xys_p)
# grab hkls and gvec ids for this panel
valid_hkls.append(allHKLs[on_panel, 1:])
valid_ids.append(allHKLs[on_panel, 0])
# reflection angles (voxel centers) and pixel size in (tth, eta)
valid_angs.append(allAngs[on_panel, :])
ang_pixel_size.append(self.angularPixelSize(xys_p))
return valid_ids, valid_hkls, valid_angs, valid_xys, ang_pixel_size
def beam_energy(self):
return keVToAngstrom(self.plane_data.wavelength)
instr_cfg_file = open('./ge_detector_new.yml', 'r')
instr_cfg = yaml.load(instr_cfg_file)
instr = instrument.HEDMInstrument(instr_cfg)
data_path = './'
img_series_root = 'ge_scan_114'
img_series = imageseries.open(
os.path.join(img_series_root + '-fcache-dir',
img_series_root + '-fcache.yml'), 'frame-cache')
nframes = 240
average_frame = imageseries.stats.average(img_series)
#%%
wlen = constants.keVToAngstrom(instr_cfg['beam']['energy'])
matl = make_matl('LSHR', 225, [
3.5905,
])
pd = matl.planeData
pd.wavelength = instr_cfg['beam']['energy'] # takes keV
pd.exclusions = np.zeros_like(pd.exclusions, dtype=bool)
set_by_tth_max = False
if set_by_tth_max:
pd.tThMax = np.radians(6.75)
tth_del = np.radians(0.75)
tth_avg = np.average(pd.getTTh())
tth_lo = pd.getTTh()[0] - tth_del