for i, experiment in enumerate(experiments):
experiment_filename = experiments_template(index=i)
print("Saving experiment %d to %s" % (i, experiment_filename))
ExperimentList([experiment]).as_json(experiment_filename)
if reflections is not None:
reflections_filename = reflections_template(index=i)
print(
"Saving reflections for experiment %d to %s"
% (i, reflections_filename)
)
ref_sel = reflections.select(reflections["id"] == i)
if ref_sel.experiment_identifiers().keys():
identifier = ref_sel.experiment_identifiers()[i]
for k in ref_sel.experiment_identifiers().keys():
del ref_sel.experiment_identifiers()[k]
ref_sel["id"] = flex.int(ref_sel.size(), 0)
ref_sel.experiment_identifiers()[0] = identifier
else:
ref_sel["id"] = flex.int(len(ref_sel), 0)
ref_sel.as_file(reflections_filename)
return
if __name__ == "__main__":
with show_mail_on_error():
script = Script()
script.run()
def run(self):
""" Process all images assigned to this thread """
params, options = self.parser.parse_args(show_diff_phil=True)
if params.input.experiment is None or \
params.input.run_num is None or \
params.input.address is None:
raise Usage(self.usage)
if params.format.file_format == "cbf":
if params.format.cbf.detz_offset is None:
raise Usage(self.usage)
elif params.format.file_format == "pickle":
if params.input.cfg is None:
raise Usage(self.usage)
else:
raise Usage(self.usage)
if not os.path.exists(params.output.output_dir):
raise Sorry("Output path not found:" + params.output.output_dir)
#Environment variable redirect for CBFLib temporary CBF_TMP_XYZ file output
if params.format.file_format == "cbf":
if params.output.tmp_output_dir is None:
tmp_dir = os.path.join(params.output.output_dir, '.tmp')
else:
tmp_dir = os.path.join(params.output.tmp_output_dir, '.tmp')
if not os.path.exists(tmp_dir):
with show_mail_on_error():
try:
os.makedirs(tmp_dir)
# Can fail if running multiprocessed - that's OK if the folder was created
except OSError as e: # In Python 2, a FileExistsError is just an OSError
if e.errno != errno.EEXIST: # If this OSError is not a FileExistsError
raise
os.environ['CBF_TMP_DIR'] = tmp_dir
# Save the paramters
self.params = params
self.options = options
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank(
) # each process in MPI has a unique id, 0-indexed
size = comm.Get_size() # size: number of processes running in this job
# set up psana
if params.input.cfg is not None:
psana.setConfigFile(params.input.cfg)
if params.input.calib_dir is not None:
psana.setOption('psana.calib-dir', params.input.calib_dir)
dataset_name = "exp=%s:run=%s:idx" % (params.input.experiment,
params.input.run_num)
if params.input.xtc_dir is not None:
dataset_name = "exp=%s:run=%s:idx:dir=%s" % (
params.input.experiment, params.input.run_num,
params.input.xtc_dir)
ds = psana.DataSource(dataset_name)
if params.format.file_format == "cbf":
src = psana.Source('DetInfo(%s)' % params.input.address)
psana_det = psana.Detector(params.input.address, ds.env())
# set this to sys.maxint to analyze all events
if params.dispatch.max_events is None:
max_events = sys.maxsize
else:
max_events = params.dispatch.max_events
for run in ds.runs():
if params.format.file_format == "cbf":
if params.format.cbf.mode == "cspad":
# load a header only cspad cbf from the slac metrology
base_dxtbx = cspad_cbf_tbx.env_dxtbx_from_slac_metrology(
run, params.input.address)
if base_dxtbx is None:
raise Sorry(
"Couldn't load calibration file for run %d" %
run.run())
elif params.format.cbf.mode == "rayonix":
# load a header only rayonix cbf from the input parameters
detector_size = rayonix_tbx.get_rayonix_detector_dimensions(
ds.env())
base_dxtbx = rayonix_tbx.get_dxtbx_from_params(
params.format.cbf.rayonix, detector_size)
# list of all events
times = run.times()
if params.dispatch.selected_events:
times = [
t for t in times
if cspad_tbx.evt_timestamp((t.seconds(), t.nanoseconds() /
1e6)) in params.input.timestamp
]
nevents = min(len(times), max_events)
# chop the list into pieces, depending on rank. This assigns each process
# events such that the get every Nth event where N is the number of processes
mytimes = [
times[i] for i in range(nevents) if (i + rank) % size == 0
]
for i in range(len(mytimes)):
evt = run.event(mytimes[i])
id = evt.get(psana.EventId)
print("Event #", i, " has id:", id)
timestamp = cspad_tbx.evt_timestamp(
cspad_tbx.evt_time(evt)) # human readable format
if timestamp is None:
print("No timestamp, skipping shot")
continue
if evt.get("skip_event") or "skip_event" in [
key.key() for key in evt.keys()
]:
print("Skipping event", timestamp)
continue
t = timestamp
s = t[0:4] + t[5:7] + t[8:10] + t[11:13] + t[14:16] + t[
17:19] + t[20:23]
print("Processing shot", s)
if params.format.file_format == "pickle":
if evt.get("skip_event"):
print("Skipping event", id)
continue
# the data needs to have already been processed and put into the event by psana
data = evt.get(params.format.pickle.out_key)
if data is None:
print("No data")
continue
# set output paths according to the templates
path = os.path.join(params.output.output_dir,
"shot-" + s + ".pickle")
print("Saving", path)
easy_pickle.dump(path, data)
elif params.format.file_format == "cbf":
if params.format.cbf.mode == "cspad":
# get numpy array, 32x185x388
data = cspad_cbf_tbx.get_psana_corrected_data(
psana_det,
evt,
use_default=False,
dark=True,
common_mode=None,
apply_gain_mask=params.format.cbf.cspad.
gain_mask_value is not None,
gain_mask_value=params.format.cbf.cspad.
gain_mask_value,
per_pixel_gain=False)
distance = cspad_tbx.env_distance(
params.input.address, run.env(),
params.format.cbf.detz_offset)
elif params.format.cbf.mode == "rayonix":
data = rayonix_tbx.get_data_from_psana_event(
evt, params.input.address)
distance = params.format.cbf.detz_offset
if distance is None:
print("No distance, skipping shot")
continue
if self.params.format.cbf.override_energy is None:
wavelength = cspad_tbx.evt_wavelength(evt)
if wavelength is None:
print("No wavelength, skipping shot")
continue
else:
wavelength = 12398.4187 / self.params.format.cbf.override_energy
# stitch together the header, data and metadata into the final dxtbx format object
if params.format.cbf.mode == "cspad":
image = cspad_cbf_tbx.format_object_from_data(
base_dxtbx,
data,
distance,
wavelength,
timestamp,
params.input.address,
round_to_int=False)
elif params.format.cbf.mode == "rayonix":
image = rayonix_tbx.format_object_from_data(
base_dxtbx, data, distance, wavelength, timestamp,
params.input.address)
path = os.path.join(params.output.output_dir,
"shot-" + s + ".cbf")
print("Saving", path)
# write the file
import pycbf
image._cbf_handle.write_widefile(path.encode(), pycbf.CBF,\
pycbf.MIME_HEADERS|pycbf.MSG_DIGEST|pycbf.PAD_4K, 0)
run.end()
ds.end()