def integrate_one_image(data, **kwargs):
from xfel.cxi.display_spots import run_one_index_core
from labelit.dptbx.error import NoAutoIndex
from libtbx.utils import Sorry
from spotfinder.exception import SpotfinderError
from labelit.exception import AutoIndexError
from iotbx.detectors.cspad_detector_formats import detector_format_version as detector_format_function
from iotbx.detectors.cspad_detector_formats import reverse_timestamp
basename = kwargs.get("integration_basename")
if (basename is None):
basename = ""
dirname = kwargs.get("integration_dirname")
if (dirname is None):
dirname = "integration"
if (not os.path.isdir(dirname)):
import errno
try:
os.makedirs(dirname)
except OSError as exc:
if exc.errno==errno.EEXIST: pass
path = os.path.join(dirname, basename \
+ data['TIMESTAMP'] \
+ ("_%05d.pickle" % data['SEQUENCE_NUMBER']))
args = ["indexing.data=dummy",
"beam_search_scope=0.5",
"lepage_max_delta = 3.0",
"spots_pickle = None",
"subgroups_pickle = None",
"refinements_pickle = None",
"rmsd_tolerance = 5.0",
"mosflm_rmsd_tolerance = 5.0",
"indexing.completeness_pickle=%s"%path,
"difflimit_sigma_cutoff=2.0",
#"indexing.open_wx_viewer=True"
]
detector_format_version = detector_format_function(
data['DETECTOR_ADDRESS'], reverse_timestamp(data['TIMESTAMP'])[0])
args += ["distl.detector_format_version=%s" % detector_format_version]
from xfel.phil_preferences import load_cxi_phil
horizons_phil = load_cxi_phil(data["xtal_target"], args)
horizons_phil.indexing.data = data
print "XFEL processing: %s"%path
try:
return run_one_index_core(horizons_phil)
except NoAutoIndex,e:
print "NoAutoIndex", data['TIMESTAMP'], e
info = e.info
called by easy_run.fully_buffered, protecting the calling program
from boost errors.
'''
import sys
from xfel.phil_preferences import load_cxi_phil
from xfel.cxi.display_spots import run_one_index_core
from libtbx import easy_pickle
if __name__ == "__main__":
# should be invoked like this: "iota.bulletproof tmppath target args"
tmppath = sys.argv[1]
target = sys.argv[2]
args = sys.argv[3:]
try:
# index the image
horizons_phil = load_cxi_phil(target, args)
info = run_one_index_core(horizons_phil)
# save specific results from the info object to be used by iota
int_final = info.last_saved_best
easy_pickle.dump(tmppath, int_final)
except Exception, e:
if hasattr(e, "classname"):
error_message = "{}: {}".format(e.classname, e[0].replace('\n',' ')[:50])
else:
error_message = "{}".format(str(e).replace('\n', ' ')[:50])
# save the error message to be picked up by iota
easy_pickle.dump(tmppath, error_message)
lines = []
linenum = 1
for line in f:
if ((line.strip() != "") and (line[0] != '.')):
if ((framenum == -1) or (framenum == linenum)):
lines.append(line)
linenum = linenum + 1
f.close()
from spotfinder.applications.xfel import cxi_phil
horizons_phil = cxi_phil.cxi_versioned_extract(args)
print "indexing..."
t0 = clock()
# indexing can be slow. would be good to save indexing info and read it back in
results = run_one_index_core(horizons_phil)
tel = clock() - t0
print "done indexing (", tel, " sec)"
latsize = latxdim * latydim * latzdim
print "Lattice size = ", latsize
lat = np.zeros(latsize, dtype=np.float32)
ct = np.zeros(latsize, dtype=np.float32)
#name_of_interest = results.organizer.Files.filenames.FN[0]
AI = results.indexing_ai
i0 = latxdim / 2 - 1
j0 = latydim / 2 - 1
k0 = latzdim / 2 - 1
mask_tag = 32767
# read input file with list of diffraction images and scale factors
f = open(ifname,"r")
lines = []
for line in f:
if ((line.strip()!="") and (line[0] != '.')):
lines.append(line)
f.close()
from spotfinder.applications.xfel import cxi_phil
horizons_phil = cxi_phil.cxi_versioned_extract(args)
print "indexing..."
t0 = clock()
# indexing can be slow. would be good to save indexing info and read it back in
results = run_one_index_core(horizons_phil)
tel = clock()-t0
print "done indexing (",tel," sec)"
latsize = latxdim*latydim*latzdim
lat = np.zeros(latsize, dtype=np.float32)
ct = np.zeros(latsize, dtype=np.float32)
#name_of_interest = results.organizer.Files.filenames.FN[0]
AI = results.indexing_ai
i0=latxdim/2-1
j0=latydim/2-1
k0=latzdim/2-1
mask_tag = 32767
# fileidx = 0
called by easy_run.fully_buffered, protecting the calling program
from boost errors.
'''
import sys
from xfel.phil_preferences import load_cxi_phil
from xfel.cxi.display_spots import run_one_index_core
from libtbx import easy_pickle
if __name__ == "__main__":
# should be invoked like this: "iota.bulletproof tmppath target args"
tmppath = sys.argv[1]
target = sys.argv[2]
args = sys.argv[3:]
try:
# index the image
horizons_phil = load_cxi_phil(target, args)
info = run_one_index_core(horizons_phil)
# save specific results from the info object to be used by iota
int_final = info.last_saved_best
easy_pickle.dump(tmppath, int_final)
except Exception, e:
if hasattr(e, "classname"):
error_message = "{}: {}".format(e.classname,
e[0].replace('\n', ' ')[:50])
else:
error_message = "{}".format(str(e).replace('\n', ' ')[:50])
# save the error message to be picked up by iota
easy_pickle.dump(tmppath, error_message)
