def test_find_orientations(example_repo_include_path,
example_repo_config_with_eta_ome_maps,
reference_orientations):
os.chdir(example_repo_include_path)
results = find_orientations(example_repo_config_with_eta_ome_maps)
orientations = results['qbar']
try:
test_utils.compare_quaternion_lists(orientations.T,
reference_orientations)
except RuntimeError as err:
pytest.fail(str(err))
def execute(args, parser):
import logging
import os
import sys
import yaml
from hexrd import config
from hexrd.findorientations import find_orientations
# make sure hkls are passed in as a list of ints
try:
if args.hkls is not None:
args.hkls = [int(i) for i in args.hkls.split(',') if i]
except AttributeError:
# called from fit-grains, hkls not passed
args.hkls = None
# configure logging to the console
log_level = logging.DEBUG if args.debug else logging.INFO
if args.quiet:
log_level = logging.ERROR
logger = logging.getLogger('hexrd')
logger.setLevel(log_level)
ch = logging.StreamHandler()
ch.setLevel(logging.CRITICAL if args.quiet else log_level)
ch.setFormatter(
logging.Formatter('%(asctime)s - %(message)s', '%y-%m-%d %H:%M:%S')
)
logger.addHandler(ch)
logger.info('=== begin find-orientations ===')
# load the configuration settings
cfg = config.open(args.yml)[0]
# prepare the analysis directory
quats_f = os.path.join(cfg.working_dir, 'accepted_orientations.dat')
if os.path.exists(quats_f) and not (args.force or args.clean):
logger.error(
'%s already exists. Change yml file or specify "force"', quats_f
)
sys.exit()
if not os.path.exists(cfg.working_dir):
os.makedirs(cfg.working_dir)
# configure logging to file
logfile = os.path.join(
cfg.working_dir,
'find-orientations.log'
)
fh = logging.FileHandler(logfile, mode='w')
fh.setLevel(log_level)
fh.setFormatter(
logging.Formatter(
'%(asctime)s - %(name)s - %(message)s',
'%m-%d %H:%M:%S'
)
)
logger.info("logging to %s", logfile)
logger.addHandler(fh)
if args.profile:
import cProfile as profile, pstats, StringIO
pr = profile.Profile()
pr.enable()
# process the data
find_orientations(cfg, hkls=args.hkls, clean=args.clean, profile=args.profile)
if args.profile:
pr.disable()
s = StringIO.StringIO()
ps = pstats.Stats(pr, stream=s).sort_stats('cumulative')
ps.print_stats(50)
logger.info('%s', s.getvalue())
# clean up the logging
fh.flush()
fh.close()
logger.removeHandler(fh)
logger.info('=== end find-orientations ===')
ch.flush()
ch.close()
logger.removeHandler(ch)
def execute(args, parser):
import logging
import os
import sys
import yaml
from hexrd import config
from hexrd.findorientations import find_orientations
# make sure hkls are passed in as a list of ints
try:
if args.hkls is not None:
args.hkls = [int(i) for i in args.hkls.split(',') if i]
except AttributeError:
# called from fit-grains, hkls not passed
args.hkls = None
# configure logging to the console
log_level = logging.DEBUG if args.debug else logging.INFO
if args.quiet:
log_level = logging.ERROR
logger = logging.getLogger('hexrd')
logger.setLevel(log_level)
ch = logging.StreamHandler()
ch.setLevel(logging.CRITICAL if args.quiet else log_level)
ch.setFormatter(
logging.Formatter('%(asctime)s - %(message)s', '%y-%m-%d %H:%M:%S'))
logger.addHandler(ch)
logger.info('=== begin find-orientations ===')
# load the configuration settings
cfg = config.open(args.yml)[0]
# ...make this an attribute in cfg?
analysis_id = '%s_%s' % (
cfg.analysis_name.strip().replace(' ', '-'),
cfg.material.active.strip().replace(' ', '-'),
)
# prepare the analysis directory
quats_f = os.path.join(cfg.working_dir,
'accepted_orientations_%s.dat' % analysis_id)
if os.path.exists(quats_f) and not (args.force or args.clean):
logger.error(
'%s already exists. Change yml file or specify "force" or "clean"',
quats_f)
sys.exit()
if not os.path.exists(cfg.working_dir):
os.makedirs(cfg.working_dir)
# configure logging to file
logfile = os.path.join(cfg.working_dir,
'find-orientations_%s.log' % analysis_id)
fh = logging.FileHandler(logfile, mode='w')
fh.setLevel(log_level)
fh.setFormatter(
logging.Formatter('%(asctime)s - %(name)s - %(message)s',
'%m-%d %H:%M:%S'))
logger.info("logging to %s", logfile)
logger.addHandler(fh)
if args.profile:
import cProfile as profile, pstats, StringIO
pr = profile.Profile()
pr.enable()
# process the data
find_orientations(cfg,
hkls=args.hkls,
clean=args.clean,
profile=args.profile)
if args.profile:
pr.disable()
s = StringIO.StringIO()
ps = pstats.Stats(pr, stream=s).sort_stats('cumulative')
ps.print_stats(50)
logger.info('%s', s.getvalue())
# clean up the logging
fh.flush()
fh.close()
logger.removeHandler(fh)
logger.info('=== end find-orientations ===')
ch.flush()
ch.close()
logger.removeHandler(ch)
def execute(args, parser):
# load the configuration settings
cfgs = config.open(args.yml)
# configure logging to the console:
log_level = logging.DEBUG if args.debug else logging.INFO
if args.quiet:
log_level = logging.ERROR
logger = logging.getLogger('hexrd')
logger.setLevel(log_level)
ch = logging.StreamHandler()
ch.setLevel(logging.CRITICAL if args.quiet else log_level)
cf = logging.Formatter('%(asctime)s - %(message)s', '%y-%m-%d %H:%M:%S')
ch.setFormatter(cf)
logger.addHandler(ch)
# if find-orientations has not already been run, do so:
quats_f = os.path.join(
cfgs[0].working_dir,
'accepted_orientations_%s.dat' % cfgs[0].analysis_id)
if os.path.exists(quats_f):
try:
qbar = np.loadtxt(quats_f).T
except (IOError):
raise (RuntimeError,
"error loading indexing results '%s'" % quats_f)
else:
logger.info("Missing %s, running find-orientations", quats_f)
logger.removeHandler(ch)
from hexrd.findorientations import find_orientations
results = find_orientations(cfgs[0])
qbar = results['qbar']
logger.addHandler(ch)
logger.info('=== begin fit-grains ===')
clobber = args.force or args.clean
for cfg in cfgs:
# prepare the analysis directory
if os.path.exists(cfg.analysis_dir) and not clobber:
logger.error(
'Analysis "%s" at %s already exists.'
' Change yml file or specify "force"', cfg.analysis_name,
cfg.analysis_dir)
sys.exit()
# make output directories
instr = cfg.instrument.hedm
if not os.path.exists(cfg.analysis_dir):
os.makedirs(cfg.analysis_dir)
for det_key in instr.detectors:
os.mkdir(os.path.join(cfg.analysis_dir, det_key))
else:
# make sure panel dirs exist under analysis dir
for det_key in instr.detectors:
if not os.path.exists(os.path.join(cfg.analysis_dir, det_key)):
os.mkdir(os.path.join(cfg.analysis_dir, det_key))
logger.info('*** begin analysis "%s" ***', cfg.analysis_name)
# configure logging to file for this particular analysis
logfile = os.path.join(cfg.working_dir, cfg.analysis_name,
'fit-grains.log')
fh = logging.FileHandler(logfile, mode='w')
fh.setLevel(log_level)
ff = logging.Formatter('%(asctime)s - %(name)s - %(message)s',
'%m-%d %H:%M:%S')
fh.setFormatter(ff)
logger.info("logging to %s", logfile)
logger.addHandler(fh)
if args.profile:
import cProfile as profile
import pstats
from io import StringIO
pr = profile.Profile()
pr.enable()
grains_filename = os.path.join(cfg.analysis_dir, 'grains.out')
# some conditions for arg handling
existing_analysis = os.path.exists(grains_filename)
new_with_estimate = not existing_analysis \
and cfg.fit_grains.estimate is not None
new_without_estimate = not existing_analysis \
and cfg.fit_grains.estimate is None
force_with_estimate = args.force \
and cfg.fit_grains.estimate is not None
force_without_estimate = args.force and cfg.fit_grains.estimate is None
# handle args
if args.clean or force_without_estimate or new_without_estimate:
# need accepted orientations from indexing in this case
if args.clean:
logger.info(
"'clean' specified; ignoring estimate and using default")
elif force_without_estimate:
logger.info(
"'force' option specified, but no initial estimate; " +
"using default")
try:
gw = instrument.GrainDataWriter(grains_filename)
for i_g, q in enumerate(qbar.T):
phi = 2 * np.arccos(q[0])
n = xfcapi.unitRowVector(q[1:])
grain_params = np.hstack(
[phi * n, cnst.zeros_3, cnst.identity_6x1])
gw.dump_grain(int(i_g), 1., 0., grain_params)
gw.close()
except (IOError):
raise (RuntimeError, "indexing results '%s' not found!" %
'accepted_orientations_' + cfg.analysis_id + '.dat')
elif force_with_estimate or new_with_estimate:
grains_filename = cfg.fit_grains.estimate
elif existing_analysis and not (clean or force):
raise (RuntimeError, "fit results '%s' exist, " % grains_filename +
"but --clean or --force options not specified")
grains_table = np.loadtxt(grains_filename, ndmin=2)
# process the data
gid_list = None
if args.grains is not None:
gid_list = [int(i) for i in args.grains.split(',')]
pass
cfg.fit_grains.qbar = qbar
fit_results = fit_grains(
cfg,
grains_table,
show_progress=not args.quiet,
ids_to_refine=gid_list,
)
if args.profile:
pr.disable()
s = StringIO.StringIO()
ps = pstats.Stats(pr, stream=s).sort_stats('cumulative')
ps.print_stats(50)
logger.info('%s', s.getvalue())
# stop logging for this particular analysis
fh.flush()
fh.close()
logger.removeHandler(fh)
logger.info('*** end analysis "%s" ***', cfg.analysis_name)
write_results(fit_results, cfg, grains_filename)
logger.info('=== end fit-grains ===')
# stop logging to the console
ch.flush()
ch.close()
logger.removeHandler(ch)
