def generate_eta_ome_maps(cfg, hkls=None, save=True):
"""
Generates the eta-omega maps specified in the input config.
"""
# extract PlaneData from config and set active hkls
plane_data = cfg.material.plane_data
# handle logic for active hkl spec
# !!!: default to all hkls defined for material,
# override with
# 1) hkls from config, if specified; or
# 2) hkls from kwarg, if specified
available_hkls = plane_data.hkls.T
active_hkls = range(len(available_hkls))
temp = cfg.find_orientations.orientation_maps.active_hkls
active_hkls = active_hkls if temp == 'all' else temp
active_hkls = hkls if hkls is not None else active_hkls
# logging output
hklseedstr = ', '.join([str(available_hkls[i]) for i in active_hkls])
logger.info("building eta_ome maps using hkls: %s", hklseedstr)
# grad imageseries dict from cfg
imsd = cfg.image_series
# handle omega period
ome_period, _ = _process_omegas(imsd)
start = timeit.default_timer()
# make eta_ome maps
eta_ome = instrument.GenerateEtaOmeMaps(
imsd,
cfg.instrument.hedm,
plane_data,
active_hkls=active_hkls,
threshold=cfg.find_orientations.orientation_maps.threshold,
ome_period=ome_period)
logger.info("\t\t...took %f seconds", timeit.default_timer() - start)
if save:
# save maps
# ???: should perhaps set default maps name at module level
map_fname = cfg.find_orientations.orientation_maps.file \
or '_'.join([cfg.analysis_id, "eta-ome_maps.npz"])
if not os.path.exists(cfg.working_dir):
os.mkdir(cfg.working_dir)
fn = os.path.join(cfg.working_dir, map_fname)
eta_ome.save(fn)
logger.info('saved eta/ome orientation maps to "%s"', fn)
return eta_ome
def get_eta_ome(cfg, clean=False):
"""Return eta-omega maps"""
# make eta_ome maps
imsd = cfg.image_series
instr = cfg.instrument.hedm
plane_data = cfg.material.plane_data
active_hkls = cfg.find_orientations.orientation_maps.active_hkls
build_map_threshold = cfg.find_orientations.orientation_maps.threshold
ome_period = np.radians(cfg.find_orientations.omega.period)
# Use existing ones if available
maps_fname = cfg.find_orientations.orientation_maps.file
if maps_fname is None:
maps_fname = "_".join(
[analysis_id(cfg),
"t" + str(build_map_threshold),
"maps.npz"]
)
if os.path.exists(maps_fname) and not clean:
print("INFO: loading existing eta_ome maps")
eta_ome = EtaOmeMaps(maps_fname)
return eta_ome
print("INFO: building eta_ome maps")
start = timeit.default_timer()
# trim plane_data to only use active hkls
if active_hkls is not None:
excl = np.ones_like(plane_data.exclusions, dtype=bool)
excl[active_hkls] = False
plane_data.exclusions = excl
eta_ome = instrument.GenerateEtaOmeMaps(
imsd, instr, plane_data,
active_hkls=active_hkls,
threshold=build_map_threshold,
ome_period=cfg.find_orientations.omega.period
)
print("INFO: ...took %f seconds" % (timeit.default_timer() - start))
# save them
eta_ome.save(maps_fname)
return eta_ome
def generate_eta_ome_maps(cfg, hkls=None):
# extract PlaneData from config and set active hkls
plane_data = cfg.material.plane_data
# handle logicl for active hkl spec
# !!!: default to all hkls defined for material,
# override with
# 1) hkls from config, if specified; or
# 2) hkls from kwarg, if specified
available_hkls = plane_data.hkls.T
active_hkls = range(len(available_hkls))
temp = cfg.find_orientations.orientation_maps.active_hkls
active_hkls = active_hkls if temp == 'all' else temp
active_hkls = hkls if hkls is not None else active_hkls
# logging output
hklseedstr = ', '.join(
[str(available_hkls[i]) for i in active_hkls]
)
logger.info(
"building eta_ome maps using hkls: %s",
hklseedstr
)
# make eta_ome maps
eta_ome = instrument.GenerateEtaOmeMaps(
cfg.image_series, cfg.instrument.hedm, plane_data,
active_hkls=active_hkls,
threshold=cfg.find_orientations.orientation_maps.threshold,
ome_period=cfg.find_orientations.omega.period)
map_fname = cfg.find_orientations.orientation_maps.file \
or '_'.join(cfg.analysis_id, 'maps.npz')
fn = os.path.join(
cfg.working_dir,
map_fname
)
fd = os.path.split(fn)[0]
if not os.path.isdir(fd):
os.makedirs(fd)
eta_ome.save(fn)
logger.info('saved eta/ome orientation maps to "%s"', fn)
return eta_ome
det_keys = instr.detectors.keys()
imsd = dict.fromkeys(det_keys)
for det_key in det_keys:
fc_file = sorted(
glob.glob(os.path.join(data_dir, fc_stem % det_key.lower())))
if len(fc_file) != 1:
raise (RuntimeError, 'cache file not found, or multiple found')
else:
ims = load_images(fc_file[0])
imsd[det_key] = OmegaImageSeries(ims)
eta_ome = instrument.GenerateEtaOmeMaps(
imsd,
instr,
pd,
active_hkls=active_hkls,
threshold=cfg.find_orientations.orientation_maps.threshold,
ome_period=cfg.find_orientations.omega.period)
grains_data = np.loadtxt(ref_grains_out)
expmaps = grains_data[:, 3:6]
quats = rot.quatOfExpMap(expmaps.T)
#%%
for i in range(0, len(expmaps)):
this_quat = quats[:, i]
qball = quaternion_ball(this_quat, mis_thresh)
test_compl = test_GOE(cfg, qball, eta_ome, eta_tol=0.25)
GOE, compl = thresh_GOE(qball, test_compl, comp_thresh)
max_frames_output_name,
'hdf5',
path='/imageseries')
#%%
# note that here maps are only used for quaternion generation
active_hkls = fiber_seeds
# omega period...
# QUESTION: necessary???
ome_period = np.radians(cfg.find_orientations.omega.period)
# make eta_ome maps
eta_ome = instrument.GenerateEtaOmeMaps(imsd,
instr,
pd,
active_hkls=active_hkls,
threshold=map_threshold)
#%%
cmap = plt.cm.hot
cmap.set_under('b')
fig, ax = plt.subplots()
i_ring = 0
this_map_f = -ndimage.filters.gaussian_laplace(
eta_ome.dataStore[i_ring],
1.0,
)
ax.imshow(this_map_f, interpolation='nearest', vmin=0.1, vmax=1.0, cmap=cmap)
labels, num_spots = ndimage.label(this_map_f > 0,
'hdf5',
path='/imageseries')
# %%
maps_fname = analysis_id + "_maps.npz"
if os.path.exists(maps_fname) and not clobber_maps:
eta_ome = EtaOmeMaps(maps_fname)
else:
print("INFO:\tbuilding eta_ome maps")
start = timeit.default_timer()
# make eta_ome maps
eta_ome = instrument.GenerateEtaOmeMaps(
imsd,
instr,
plane_data,
active_hkls=active_hkls,
threshold=build_map_threshold,
ome_period=cfg.find_orientations.omega.period)
print("INFO:\t\t...took %f seconds" % (timeit.default_timer() - start))
# save them
eta_ome.save(maps_fname)
# %%
# =============================================================================
# OPTINAL PLOTTING
# =============================================================================
if show_maps:
cmap = plt.cm.hot