def pull_spots(self, grain_id, grain_params, iteration):
# need to calc panel dims on the fly
xdim = self._p['pixel_pitch'][1] * self._p['ncols']
ydim = self._p['pixel_pitch'][0] * self._p['nrows']
panel_dims = [(-0.5*xdim, -0.5*ydim),
( 0.5*xdim, 0.5*ydim)]
return pullSpots(
self._p['plane_data'],
self._p['detector_params'],
grain_params,
self._reader,
distortion=self._p['distortion'],
eta_range=self._p['eta_range'],
ome_period=self._p['omega_period'],
eta_tol=self._p['eta_tol'][iteration],
ome_tol=self._p['omega_tol'][iteration],
tth_tol=self._p['tth_tol'][iteration],
pixel_pitch=self._p['pixel_pitch'],
panel_dims=panel_dims,
panel_buff=self._p['panel_buffer'],
npdiv=self._p['npdiv'],
threshold=self._p['threshold'],
doClipping=False,
filename=self._p['spots_stem'] % grain_id,
)
def pull_spots(self, grain_id, grain_params, iteration):
return pullSpots(
self._p['plane_data'],
self._p['detector_params'],
grain_params,
self._reader,
distortion=self._p['distortion'],
eta_range=self._p['eta_range'],
ome_period=self._p['omega_period'],
eta_tol=self._p['eta_tol'][iteration],
ome_tol=self._p['omega_tol'][iteration],
tth_tol=self._p['tth_tol'][iteration],
panel_buff=self._p['panel_buffer'],
npdiv=self._p['npdiv'],
threshold=self._p['threshold'],
doClipping=False,
filename=self._p['spots_stem'] % grain_id,
)
def pull_spots(self, grain_id, grain_params, iteration, output_hdf5=False):
# need to calc panel dims on the fly
xdim = self._p['pixel_pitch'][1] * self._p['ncols']
ydim = self._p['pixel_pitch'][0] * self._p['nrows']
panel_dims = [(-0.5 * xdim, -0.5 * ydim), (0.5 * xdim, 0.5 * ydim)]
return pullSpots(self._p['plane_data'],
self._p['detector_params'],
grain_params,
self._reader,
distortion=self._p['distortion'],
eta_range=self._p['eta_range'],
ome_period=self._p['omega_period'],
eta_tol=self._p['eta_tol'][iteration],
ome_tol=self._p['omega_tol'][iteration],
tth_tol=self._p['tth_tol'][iteration],
pixel_pitch=self._p['pixel_pitch'],
panel_dims=panel_dims,
panel_buff=self._p['panel_buffer'],
npdiv=self._p['npdiv'],
threshold=self._p['threshold'],
doClipping=False,
filename=self._p['spots_stem'] % grain_id,
output_hdf5=output_hdf5)
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,
distortion=distortion)
pass
if have_progBar:
pbar.finish()
pass
pass # condidional on pull spots
pass
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,
distortion=distortion)
pass
if have_progBar:
pbar.finish()
pass
pass # condidional on pull spots
pass
"tVec_c[0]\ttVec_c[1]\ttVec_c[2]\t" + \
"vInv_s[0]\tvInv_s[1]\tvInv_s[2]\tvInv_s[4]*sqrt(2)\tvInv_s[5]*sqrt(2)\tvInv_s[6]*sqrt(2)\t" + \
"ln(V[0,0])\tln(V[1,1])\tln(V[2,2])\tln(V[1,2])\tln(V[0,2])\tln(V[0,1])"
# loop over grains from previous fit
for grainID in range(n_grains):
start = time.clock() # time this
print "fitting %d" %grainID
#
grain_params = gp_table[grainID, 3:15]
#
fid = open(filename %grainID, 'w')
sd = xrdutil.pullSpots(pd, detector_params, grain_params, reader,
distortion=(dFunc, dParams),
eta_range=etaRange, ome_period=ome_period,
tth_tol=tth_tol, eta_tol=eta_tol, ome_tol=ome_tol,
panel_buff=[10, 10],
npdiv=2, threshold=threshold, doClipping=False,
filename=fid)
fid.close()
# strain fitting
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:
