def test_cellcentroids(in_file):
count = 0
with open(in_file, 'rb') as f:
while True:
try:
args = pickle.load(f)
except EOFError:
break
with nvtx.profile_range('original'):
res_orig = cell_centroids_original(*args)
with nvtx.profile_range('current in hexrd'):
res_current = cellCentroids(*args)
with nvtx.profile_range('numba1'):
res_numba1 = cell_centroids_opt1(*args)
with nvtx.profile_range('numba1_bis'):
res_numba1 = cell_centroids_opt1(*args)
with nvtx.profile_range('numba'):
res_numba = cell_centroids_numba(*args)
with nvtx.profile_range('numba_bis'):
res_numba = cell_centroids_numba(*args)
assert np.allclose(res_current, res_orig)
assert np.allclose(res_current, res_numba1)
assert np.allclose(res_current, res_numba)
count += 1
def test_cellcentroids(in_file):
count = 0
with open(in_file, 'rb') as f:
while True:
try:
args = pickle.load(f)
except EOFError:
break
with nvtx.profile_range('original'):
res_orig = cell_centroids_original(*args)
with nvtx.profile_range('current in hexrd'):
res_current = cellCentroids(*args)
with nvtx.profile_range('numba1'):
res_numba1 = cell_centroids_opt1(*args)
with nvtx.profile_range('numba1_bis'):
res_numba1 = cell_centroids_opt1(*args)
with nvtx.profile_range('numba'):
res_numba = cell_centroids_numba(*args)
with nvtx.profile_range('numba_bis'):
res_numba = cell_centroids_numba(*args)
assert np.allclose(res_current, res_orig)
assert np.allclose(res_current, res_numba1)
assert np.allclose(res_current, res_numba)
count += 1
def make_reflection_patches(instr_cfg,
tth_eta,
ang_pixel_size,
omega=None,
tth_tol=0.2,
eta_tol=1.0,
rMat_c=np.eye(3),
tVec_c=np.c_[0., 0., 0.].T,
distortion=distortion,
npdiv=1,
quiet=False,
compute_areas_func=compute_areas):
"""
prototype function for making angular patches on a detector
panel_dims are [(xmin, ymin), (xmax, ymax)] in mm
pixel_pitch is [row_size, column_size] in mm
DISTORTION HANDING IS STILL A KLUDGE
patches are:
delta tth
d ------------- ... -------------
e | x | x | x | ... | x | x | x |
l ------------- ... -------------
t .
a .
.
e ------------- ... -------------
t | x | x | x | ... | x | x | x |
a ------------- ... -------------
"""
npts = len(tth_eta)
# detector frame
rMat_d = xfcapi.makeDetectorRotMat(
instr_cfg['detector']['transform']['tilt_angles'])
tVec_d = np.r_[instr_cfg['detector']['transform']['t_vec_d']]
pixel_size = instr_cfg['detector']['pixels']['size']
frame_nrows = instr_cfg['detector']['pixels']['rows']
frame_ncols = instr_cfg['detector']['pixels']['columns']
panel_dims = (
-0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]],
0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]])
row_edges = np.arange(frame_nrows +
1)[::-1] * pixel_size[1] + panel_dims[0][1]
col_edges = np.arange(frame_ncols + 1) * pixel_size[0] + panel_dims[0][0]
# sample frame
chi = instr_cfg['oscillation_stage']['chi']
tVec_s = np.r_[instr_cfg['oscillation_stage']['t_vec_s']]
# data to loop
# ...WOULD IT BE CHEAPER TO CARRY ZEROS OR USE CONDITIONAL?
if omega is None:
full_angs = np.hstack([tth_eta, np.zeros((npts, 1))])
else:
full_angs = np.hstack([tth_eta, omega.reshape(npts, 1)])
patches = []
for angs, pix in zip(full_angs, ang_pixel_size):
# need to get angular pixel size
rMat_s = xfcapi.makeOscillRotMat([chi, angs[2]])
ndiv_tth = npdiv * np.ceil(tth_tol / np.degrees(pix[0]))
ndiv_eta = npdiv * np.ceil(eta_tol / np.degrees(pix[1]))
tth_del = np.arange(
0, ndiv_tth + 1) * tth_tol / float(ndiv_tth) - 0.5 * tth_tol
eta_del = np.arange(
0, ndiv_eta + 1) * eta_tol / float(ndiv_eta) - 0.5 * eta_tol
# store dimensions for convenience
# * etas and tths are bin vertices, ome is already centers
sdims = [len(eta_del) - 1, len(tth_del) - 1]
# meshgrid args are (cols, rows), a.k.a (fast, slow)
m_tth, m_eta = np.meshgrid(tth_del, eta_del)
npts_patch = m_tth.size
# calculate the patch XY coords from the (tth, eta) angles
# * will CHEAT and ignore the small perturbation the different
# omega angle values causes and simply use the central value
gVec_angs_vtx = np.tile(angs, (npts_patch, 1)) \
+ np.radians(
np.vstack([m_tth.flatten(),
m_eta.flatten(),
np.zeros(npts_patch)
]).T
)
# will need this later
rMat_s = xfcapi.makeOscillRotMat([chi, angs[2]])
# FOR ANGULAR MESH
conn = gutil.cellConnectivity(sdims[0], sdims[1], origin='ll')
gVec_c = xf.anglesToGVec(gVec_angs_vtx,
xf.bVec_ref,
xf.eta_ref,
rMat_s=rMat_s,
rMat_c=rMat_c)
xy_eval_vtx = xfcapi.gvecToDetectorXY(gVec_c.T, rMat_d, rMat_s, rMat_c,
tVec_d, tVec_s, tVec_c)
if distortion is not None and len(distortion) == 2:
xy_eval_vtx = distortion[0](xy_eval_vtx,
distortion[1],
invert=True)
pass
areas = compute_areas_func(xy_eval_vtx, conn)
# EVALUATION POINTS
# * for lack of a better option will use centroids
tth_eta_cen = gutil.cellCentroids(np.atleast_2d(gVec_angs_vtx[:, :2]),
conn)
gVec_angs = np.hstack(
[tth_eta_cen, np.tile(angs[2], (len(tth_eta_cen), 1))])
gVec_c = xf.anglesToGVec(gVec_angs,
xf.bVec_ref,
xf.eta_ref,
rMat_s=rMat_s,
rMat_c=rMat_c)
xy_eval = xfcapi.gvecToDetectorXY(gVec_c.T, rMat_d, rMat_s, rMat_c,
tVec_d, tVec_s, tVec_c)
if distortion is not None and len(distortion) == 2:
xy_eval = distortion[0](xy_eval, distortion[1], invert=True)
pass
row_indices = gutil.cellIndices(row_edges, xy_eval[:, 1])
col_indices = gutil.cellIndices(col_edges, xy_eval[:, 0])
patches.append(
((gVec_angs_vtx[:, 0].reshape(m_tth.shape),
gVec_angs_vtx[:, 1].reshape(m_tth.shape)),
(xy_eval_vtx[:, 0].reshape(m_tth.shape),
xy_eval_vtx[:, 1].reshape(m_tth.shape)), conn,
areas.reshape(sdims[0],
sdims[1]), (row_indices.reshape(sdims[0], sdims[1]),
col_indices.reshape(sdims[0],
sdims[1]))))
pass
return patches
def make_reflection_patches(instr_cfg,
tth_eta,
ang_pixel_size,
omega=None,
tth_tol=0.2,
eta_tol=1.0,
rMat_c=np.eye(3),
tVec_c=np.zeros((3, 1)),
distortion=None,
npdiv=1,
quiet=False,
compute_areas_func=gutil.compute_areas,
beamVec=None):
"""
prototype function for making angular patches on a detector
panel_dims are [(xmin, ymin), (xmax, ymax)] in mm
pixel_pitch is [row_size, column_size] in mm
FIXME: DISTORTION HANDING IS STILL A KLUDGE!!!
patches are:
delta tth
d ------------- ... -------------
e | x | x | x | ... | x | x | x |
l ------------- ... -------------
t .
a .
.
e ------------- ... -------------
t | x | x | x | ... | x | x | x |
a ------------- ... -------------
outputs are:
(tth_vtx, eta_vtx),
(x_vtx, y_vtx),
connectivity,
subpixel_areas,
(x_center, y_center),
(i_row, j_col)
"""
npts = len(tth_eta)
# detector frame
rMat_d = xfcapi.makeRotMatOfExpMap(
np.r_[instr_cfg['detector']['transform']['tilt']])
tVec_d = np.r_[instr_cfg['detector']['transform']['translation']]
pixel_size = instr_cfg['detector']['pixels']['size']
frame_nrows = instr_cfg['detector']['pixels']['rows']
frame_ncols = instr_cfg['detector']['pixels']['columns']
panel_dims = (
-0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]],
0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]])
row_edges = np.arange(frame_nrows + 1)[::-1]*pixel_size[1] \
+ panel_dims[0][1]
col_edges = np.arange(frame_ncols + 1)*pixel_size[0] \
+ panel_dims[0][0]
# sample frame
chi = instr_cfg['oscillation_stage']['chi']
tVec_s = np.r_[instr_cfg['oscillation_stage']['translation']]
# beam vector
if beamVec is None:
beamVec = xfcapi.bVec_ref
# data to loop
# ...WOULD IT BE CHEAPER TO CARRY ZEROS OR USE CONDITIONAL?
if omega is None:
full_angs = np.hstack([tth_eta, np.zeros((npts, 1))])
else:
full_angs = np.hstack([tth_eta, omega.reshape(npts, 1)])
patches = []
for angs, pix in zip(full_angs, ang_pixel_size):
ndiv_tth = npdiv * np.ceil(tth_tol / np.degrees(pix[0]))
ndiv_eta = npdiv * np.ceil(eta_tol / np.degrees(pix[1]))
tth_del = np.arange(0, ndiv_tth + 1)*tth_tol/float(ndiv_tth) \
- 0.5*tth_tol
eta_del = np.arange(0, ndiv_eta + 1)*eta_tol/float(ndiv_eta) \
- 0.5*eta_tol
# store dimensions for convenience
# * etas and tths are bin vertices, ome is already centers
sdims = [len(eta_del) - 1, len(tth_del) - 1]
# FOR ANGULAR MESH
conn = gutil.cellConnectivity(sdims[0], sdims[1], origin='ll')
# meshgrid args are (cols, rows), a.k.a (fast, slow)
m_tth, m_eta = np.meshgrid(tth_del, eta_del)
npts_patch = m_tth.size
# calculate the patch XY coords from the (tth, eta) angles
# * will CHEAT and ignore the small perturbation the different
# omega angle values causes and simply use the central value
gVec_angs_vtx = np.tile(angs, (npts_patch, 1)) \
+ np.radians(
np.vstack(
[m_tth.flatten(),
m_eta.flatten(),
np.zeros(npts_patch)]
).T
)
xy_eval_vtx, _ = _project_on_detector_plane(gVec_angs_vtx,
rMat_d,
rMat_c,
chi,
tVec_d,
tVec_c,
tVec_s,
distortion,
beamVec=beamVec)
areas = compute_areas_func(xy_eval_vtx, conn)
# EVALUATION POINTS
# * for lack of a better option will use centroids
tth_eta_cen = gutil.cellCentroids(np.atleast_2d(gVec_angs_vtx[:, :2]),
conn)
gVec_angs = np.hstack(
[tth_eta_cen, np.tile(angs[2], (len(tth_eta_cen), 1))])
xy_eval, _ = _project_on_detector_plane(gVec_angs,
rMat_d,
rMat_c,
chi,
tVec_d,
tVec_c,
tVec_s,
distortion,
beamVec=beamVec)
row_indices = gutil.cellIndices(row_edges, xy_eval[:, 1])
col_indices = gutil.cellIndices(col_edges, xy_eval[:, 0])
# append patch data to list
patches.append(
((gVec_angs_vtx[:, 0].reshape(m_tth.shape),
gVec_angs_vtx[:, 1].reshape(m_tth.shape)),
(xy_eval_vtx[:, 0].reshape(m_tth.shape),
xy_eval_vtx[:, 1].reshape(m_tth.shape)), conn,
areas.reshape(sdims[0],
sdims[1]), (xy_eval[:,
0].reshape(sdims[0], sdims[1]),
xy_eval[:,
1].reshape(sdims[0], sdims[1])),
(row_indices.reshape(sdims[0], sdims[1]),
col_indices.reshape(sdims[0], sdims[1]))))
pass # close loop over angles
return patches
def make_reflection_patches(
instr_cfg,
tth_eta,
ang_pixel_size,
omega=None,
tth_tol=0.2,
eta_tol=1.0,
rMat_c=np.eye(3),
tVec_c=np.c_[0.0, 0.0, 0.0].T,
distortion=distortion,
npdiv=1,
quiet=False,
compute_areas_func=compute_areas,
):
"""
prototype function for making angular patches on a detector
panel_dims are [(xmin, ymin), (xmax, ymax)] in mm
pixel_pitch is [row_size, column_size] in mm
DISTORTION HANDING IS STILL A KLUDGE
patches are:
delta tth
d ------------- ... -------------
e | x | x | x | ... | x | x | x |
l ------------- ... -------------
t .
a .
.
e ------------- ... -------------
t | x | x | x | ... | x | x | x |
a ------------- ... -------------
"""
npts = len(tth_eta)
# detector frame
rMat_d = xfcapi.makeDetectorRotMat(instr_cfg["detector"]["transform"]["tilt_angles"])
tVec_d = np.r_[instr_cfg["detector"]["transform"]["t_vec_d"]]
pixel_size = instr_cfg["detector"]["pixels"]["size"]
frame_nrows = instr_cfg["detector"]["pixels"]["rows"]
frame_ncols = instr_cfg["detector"]["pixels"]["columns"]
panel_dims = (
-0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]],
0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]],
)
row_edges = np.arange(frame_nrows + 1)[::-1] * pixel_size[1] + panel_dims[0][1]
col_edges = np.arange(frame_ncols + 1) * pixel_size[0] + panel_dims[0][0]
# sample frame
chi = instr_cfg["oscillation_stage"]["chi"]
tVec_s = np.r_[instr_cfg["oscillation_stage"]["t_vec_s"]]
# data to loop
# ...WOULD IT BE CHEAPER TO CARRY ZEROS OR USE CONDITIONAL?
if omega is None:
full_angs = np.hstack([tth_eta, np.zeros((npts, 1))])
else:
full_angs = np.hstack([tth_eta, omega.reshape(npts, 1)])
patches = []
for angs, pix in zip(full_angs, ang_pixel_size):
# need to get angular pixel size
rMat_s = xfcapi.makeOscillRotMat([chi, angs[2]])
ndiv_tth = npdiv * np.ceil(tth_tol / np.degrees(pix[0]))
ndiv_eta = npdiv * np.ceil(eta_tol / np.degrees(pix[1]))
tth_del = np.arange(0, ndiv_tth + 1) * tth_tol / float(ndiv_tth) - 0.5 * tth_tol
eta_del = np.arange(0, ndiv_eta + 1) * eta_tol / float(ndiv_eta) - 0.5 * eta_tol
# store dimensions for convenience
# * etas and tths are bin vertices, ome is already centers
sdims = [len(eta_del) - 1, len(tth_del) - 1]
# meshgrid args are (cols, rows), a.k.a (fast, slow)
m_tth, m_eta = np.meshgrid(tth_del, eta_del)
npts_patch = m_tth.size
# calculate the patch XY coords from the (tth, eta) angles
# * will CHEAT and ignore the small perturbation the different
# omega angle values causes and simply use the central value
gVec_angs_vtx = np.tile(angs, (npts_patch, 1)) + np.radians(
np.vstack([m_tth.flatten(), m_eta.flatten(), np.zeros(npts_patch)]).T
)
# will need this later
rMat_s = xfcapi.makeOscillRotMat([chi, angs[2]])
# FOR ANGULAR MESH
conn = gutil.cellConnectivity(sdims[0], sdims[1], origin="ll")
gVec_c = xf.anglesToGVec(gVec_angs_vtx, xf.bVec_ref, xf.eta_ref, rMat_s=rMat_s, rMat_c=rMat_c)
xy_eval_vtx = xfcapi.gvecToDetectorXY(gVec_c.T, rMat_d, rMat_s, rMat_c, tVec_d, tVec_s, tVec_c)
if distortion is not None and len(distortion) == 2:
xy_eval_vtx = distortion[0](xy_eval_vtx, distortion[1], invert=True)
pass
areas = compute_areas_func(xy_eval_vtx, conn)
# EVALUATION POINTS
# * for lack of a better option will use centroids
tth_eta_cen = gutil.cellCentroids(np.atleast_2d(gVec_angs_vtx[:, :2]), conn)
gVec_angs = np.hstack([tth_eta_cen, np.tile(angs[2], (len(tth_eta_cen), 1))])
gVec_c = xf.anglesToGVec(gVec_angs, xf.bVec_ref, xf.eta_ref, rMat_s=rMat_s, rMat_c=rMat_c)
xy_eval = xfcapi.gvecToDetectorXY(gVec_c.T, rMat_d, rMat_s, rMat_c, tVec_d, tVec_s, tVec_c)
if distortion is not None and len(distortion) == 2:
xy_eval = distortion[0](xy_eval, distortion[1], invert=True)
pass
row_indices = gutil.cellIndices(row_edges, xy_eval[:, 1])
col_indices = gutil.cellIndices(col_edges, xy_eval[:, 0])
patches.append(
(
(gVec_angs_vtx[:, 0].reshape(m_tth.shape), gVec_angs_vtx[:, 1].reshape(m_tth.shape)),
(xy_eval_vtx[:, 0].reshape(m_tth.shape), xy_eval_vtx[:, 1].reshape(m_tth.shape)),
conn,
areas.reshape(sdims[0], sdims[1]),
(row_indices.reshape(sdims[0], sdims[1]), col_indices.reshape(sdims[0], sdims[1])),
)
)
pass
return patches
def make_reflection_patches(instr_cfg,
tth_eta,
ang_pixel_size,
omega=None,
tth_tol=0.2,
eta_tol=1.0,
rmat_c=np.eye(3),
tvec_c=np.zeros((3, 1)),
npdiv=1,
quiet=False,
compute_areas_func=gutil.compute_areas):
"""
Make angular patches on a detector.
panel_dims are [(xmin, ymin), (xmax, ymax)] in mm
pixel_pitch is [row_size, column_size] in mm
FIXME: DISTORTION HANDING IS STILL A KLUDGE!!!
patches are:
delta tth
d ------------- ... -------------
e | x | x | x | ... | x | x | x |
l ------------- ... -------------
t .
a .
.
e ------------- ... -------------
t | x | x | x | ... | x | x | x |
a ------------- ... -------------
outputs are:
(tth_vtx, eta_vtx),
(x_vtx, y_vtx),
connectivity,
subpixel_areas,
(x_center, y_center),
(i_row, j_col)
"""
npts = len(tth_eta)
# detector quantities
rmat_d = xfcapi.makeRotMatOfExpMap(
np.r_[instr_cfg['detector']['transform']['tilt']])
tvec_d = np.r_[instr_cfg['detector']['transform']['translation']]
pixel_size = instr_cfg['detector']['pixels']['size']
frame_nrows = instr_cfg['detector']['pixels']['rows']
frame_ncols = instr_cfg['detector']['pixels']['columns']
panel_dims = (
-0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]],
0.5 * np.r_[frame_ncols * pixel_size[1], frame_nrows * pixel_size[0]])
row_edges = np.arange(frame_nrows + 1)[::-1]*pixel_size[1] \
+ panel_dims[0][1]
col_edges = np.arange(frame_ncols + 1)*pixel_size[0] \
+ panel_dims[0][0]
# handle distortion
distortion = None
if distortion_key in instr_cfg['detector']:
distortion_cfg = instr_cfg['detector'][distortion_key]
if distortion_cfg is not None:
try:
func_name = distortion_cfg['function_name']
dparams = distortion_cfg['parameters']
distortion = distortion_pkg.get_mapping(func_name, dparams)
except (KeyError):
raise RuntimeError("problem with distortion specification")
# sample frame
chi = instr_cfg['oscillation_stage']['chi']
tvec_s = np.r_[instr_cfg['oscillation_stage']['translation']]
# beam vector
bvec = np.r_[instr_cfg['beam']['vector']]
# data to loop
# ??? WOULD IT BE CHEAPER TO CARRY ZEROS OR USE CONDITIONAL?
if omega is None:
full_angs = np.hstack([tth_eta, np.zeros((npts, 1))])
else:
full_angs = np.hstack([tth_eta, omega.reshape(npts, 1)])
patches = []
for angs, pix in zip(full_angs, ang_pixel_size):
# calculate bin edges for patch based on local angular pixel size
# tth
ntths, tth_edges = gutil.make_tolerance_grid(bin_width=np.degrees(
pix[0]),
window_width=tth_tol,
num_subdivisions=npdiv)
# eta
netas, eta_edges = gutil.make_tolerance_grid(bin_width=np.degrees(
pix[1]),
window_width=eta_tol,
num_subdivisions=npdiv)
# FOR ANGULAR MESH
conn = gutil.cellConnectivity(netas, ntths, origin='ll')
# meshgrid args are (cols, rows), a.k.a (fast, slow)
m_tth, m_eta = np.meshgrid(tth_edges, eta_edges)
npts_patch = m_tth.size
# calculate the patch XY coords from the (tth, eta) angles
# !!! will CHEAT and ignore the small perturbation the different
# omega angle values causes and simply use the central value
gVec_angs_vtx = np.tile(angs, (npts_patch, 1)) \
+ np.radians(
np.vstack([m_tth.flatten(),
m_eta.flatten(),
np.zeros(npts_patch)
]).T
)
xy_eval_vtx, rmats_s, on_plane = _project_on_detector_plane(
gVec_angs_vtx,
rmat_d,
rmat_c,
chi,
tvec_d,
tvec_c,
tvec_s,
distortion,
beamVec=bvec)
areas = compute_areas_func(xy_eval_vtx, conn)
# EVALUATION POINTS
# !!! for lack of a better option will use centroids
tth_eta_cen = gutil.cellCentroids(np.atleast_2d(gVec_angs_vtx[:, :2]),
conn)
gVec_angs = np.hstack(
[tth_eta_cen, np.tile(angs[2], (len(tth_eta_cen), 1))])
xy_eval, rmats_s, on_plane = _project_on_detector_plane(gVec_angs,
rmat_d,
rmat_c,
chi,
tvec_d,
tvec_c,
tvec_s,
distortion,
beamVec=bvec)
row_indices = gutil.cellIndices(row_edges, xy_eval[:, 1])
col_indices = gutil.cellIndices(col_edges, xy_eval[:, 0])
# append patch data to list
patches.append(
((gVec_angs_vtx[:, 0].reshape(m_tth.shape),
gVec_angs_vtx[:, 1].reshape(m_tth.shape)),
(xy_eval_vtx[:, 0].reshape(m_tth.shape),
xy_eval_vtx[:, 1].reshape(m_tth.shape)), conn,
areas.reshape(netas, ntths), (xy_eval[:, 0].reshape(netas, ntths),
xy_eval[:, 1].reshape(netas,
ntths)),
(row_indices.reshape(netas,
ntths), col_indices.reshape(netas, ntths))))
pass # close loop over angles
return patches
