def get_versions():
from dials.util.version import dials_version
from i19.util.version import i19_version
import xia2.XIA2Version
versions = {
'xia2': xia2.XIA2Version.Version,
'dials': dials_version(),
'i19': i19_version(),
'aimless': 'AIMLESS, CCP4' }
with open(find_aimless_log(), 'r') as aimlesslog:
pattern = re.compile(" +#+ *CCP4.*#+")
for line in aimlesslog:
if pattern.search(line):
versions['aimless'] = re.sub('\s\s+', ', ', line.strip("\t\n #"))
break
return versions
from __future__ import division try: import i19.util.version as version print version.i19_version() except ImportError: pass
def run(self, args):
from dials.util.version import dials_version
from i19.util.version import i19_version
version_information = "%s using %s (%s)" % (i19_version(), dials_version(), time.strftime("%Y-%m-%d %H:%M:%S"))
start = timeit.default_timer()
if len(args) == 0:
print help_message
print version_information
return
# Configure the logging
from dials.util import log
log.config(1, info='i19.screen.log', debug='i19.screen.debug.log')
info(version_information)
debug('Run with %s' % str(args))
# FIXME use proper optionparser here. This works for now
nproc = None
if len(args) >= 1 and args[0].startswith('nproc='):
nproc = args[0][6:]
args = args[1:]
self._count_processors(nproc=nproc)
debug('Using %s processors' % self.nproc)
if len(args) == 1 and args[0].endswith('.json'):
self.json_file = args[0]
else:
self._import(args)
self.json_file = 'datablock.json'
self._find_spots()
if not self._index():
info("\nRetrying for stronger spots only...")
os.rename("strong.pickle", "all_spots.pickle")
self._find_spots(['sigma_strong=15'])
if not self._index():
warn("Giving up.")
info("""
Could not find an indexing solution. You may want to have a look
at the reciprocal space by running:
dials.reciprocal_lattice_viewer datablock.json all_spots.pickle
or, to only include stronger spots:
dials.reciprocal_lattice_viewer datablock.json strong.pickle
""")
sys.exit(1)
if not self._create_profile_model():
info("\nRefining model to attempt to increase number of valid spots...")
self._refine()
if not self._create_profile_model():
warn("Giving up.")
info("""
The identified indexing solution may not be correct. You may want to have a look
at the reciprocal space by running:
dials.reciprocal_lattice_viewer experiments.json indexed.pickle
""")
sys.exit(1)
self._report()
self._predict()
self._check_intensities()
self._refine_bravais()
i19screen_runtime = timeit.default_timer() - start
debug("Finished at %s, total runtime: %.1f" % (time.strftime("%Y-%m-%d %H:%M:%S"), i19screen_runtime))
info("i19.screen successfully completed (%.1f sec)" % i19screen_runtime)