def process_event(run, evt, psana_det):
"""
Process a single event from a run
@param run psana run object
@param timestamp psana timestamp object
"""
# HACK: Force psana v2 behaviour
PSANA2_VERSION = True
start("construct event timestamp")
if PSANA2_VERSION:
sec = evt._seconds
nsec = evt._nanoseconds
else:
time = evt.get(psana.EventId).time()
fid = evt.get(psana.EventId).fiducials()
sec = time[0]
nsec = time[1]
ts = Event.as_timestamp(sec, nsec / 1e6)
stop("construct event timestamp")
print("Accepted", ts)
# HACK: these parameters have been extracted from a xtc_process run
data = get_psana_corrected_data(psana_det,
evt,
use_default=False,
dark=True,
common_mode=None,
apply_gain_mask=True,
gain_mask_value=6.85,
per_pixel_gain=False,
additional_gain_factor=None)
if data is None:
print("ERROR! No data")
return
timestamp = t = ts
s = t[0:4] + t[5:7] + t[8:10] + t[11:13] + t[14:16] + t[17:19] + t[20:23]
print("Loaded shot", s)
def bcast_dials_mask(comm, invalid_pixel_mask_path):
if comm.Get_rank() == 0:
# Check if environment variables are defined <-- I don't know what this
# is good for, but the original xtc_process.py has it
start("get_environ")
PS_CALIB_DIR = os.environ.get('PS_CALIB_DIR')
assert PS_CALIB_DIR
stop("get_environ")
# Load pickle -- this is different from CCTBX because there we're using
# easy_pickle <-- I am not importing easy_pickle because I don't want
# to enter dependency hell
start("load_invalid_pixel_mask")
with open(invalid_pixel_mask_path, "rb") as f:
dials_mask = load(f)
stop("load_invalid_pixel_mask")
else:
dials_mask = None
# Bcast the dials_mask array
start("bcast_dials_mask")
dials_mask = comm.bcast(dials_mask, root=0)
stop("bcast_dials_mask")
return dials_mask
def get_calib_file_path(env, address, run):
""" Findes the path to the SLAC metrology file stored in a psana
environment object's calibration store
@param env psana environment object
@param address address string for a detector
@param run psana run object or run number
"""
from psana import Detector
#
# try to get it from the detector interface
#
try:
start("load geometry from detector")
psana_det = Detector(address, run.env())
ret = psana_det.pyda.geoaccess(run.run()).path
stop("load geometry from detector")
return ret
except Exception as e:
pass
#
# try to get it from the calib store directly
#
from psana import ndarray_uint8_1, Source
start("load geometry from calib store")
cls = env.calibStore()
src = Source('DetInfo(%s)' % address)
path_nda = cls.get(ndarray_uint8_1, src, 'geometry-calib')
stop("load geometry from calib store")
if path_nda is None:
return None
return ''.join(map(chr, path_nda))
def test_xtc_read(ds, comm, det_name):
for run in ds.runs():
start(f"run.Detector({ds.det_name})")
det = run.Detector(ds.det_name)
stop(f"run.Detector({ds.det_name})")
# TODO: fix flex dependency
# if comm.Get_rank() == 0:
# PS_CALIB_DIR = os.environ.get('PS_CALIB_DIR')
# assert PS_CALIB_DIR
# dials_mask = easy_pickle.load(params.format.cbf.invalid_pixel_mask)
# else:
# dials_mask = None
# dials_mask = comm.bcast(dials_mask, root=0)
start("for evt in run.events()")
for evt in run.events():
env_dxtbx_from_slac_metrology(run, det_name)
process_event(run, evt, det)
stop("for evt in run.events()")
def env_dxtbx_from_slac_metrology(run, address):
""" Loads a dxtbx cspad cbf header only object from the metrology path
stored in a psana run object's calibration store
@param env psana run object
@param address address string for a detector
"""
start("load geometry data from detector")
det = run.Detector(address)
geometry = det.raw.geometry()
stop("load geometry data from detector")
if geometry is None:
metro_path = get_calib_file_path(run.env(), address, run)
elif geometry.valid:
metro_path = None
else:
raise RuntimeError(
f"Could not read geometry, hostname: {socket.gethostname()}")
if metro_path is None and geometry is None:
return None
return None
def test_inplace_logger(n):
start("sleep({n})")
sleep(n) # sleep for n seconds
stop("sleep")
parser.add_argument("--invalid_pixel_mask_path",
help="Path the the invalid pixel mask pickle file")
parser.add_argument(
"--of", help="Log dir -- every rank will write its own log file")
# Get args dict, and sanitize None types
args = vars(parser.parse_args())
output_name = args["of"]
invalid_pixel_mask_path = args["invalid_pixel_mask_path"]
#
# Initialize MPI
#
start("INIT MPI")
from mpi4py import MPI
comm = MPI.COMM_WORLD
stop("INIT MPI")
rank = comm.Get_rank() # each process in MPI has a unique id, 0-indexed
#
# Run Benchmark
#
if rank == 0:
print("MPI Initialize, Running bcast_dials_mask Benchmark")
bcast_dials_mask(comm, invalid_pixel_mask_path)
def run():
print "generating 50,000 users..."
iusers = []
[iusers.append(i) for i in range(0, 50000, 1)]
print "users generated...benchmarking."
print "loading modules.."
benchmarking.start("load modules")
import core
from core import var, database
benchmarking.stop("load modules")
print "initializing db.."
benchmarking.start("init db")
db = database.Database()
benchmarking.stop("init db")
print "registering a user.."
benchmarking.start("reg one user")
db.register_user("user", "pasword")
benchmarking.stop("reg one user")
print "modifying user metadata.."
benchmarking.start("modify user metadata")
db.__refero__()["users"]["user"]["metadata"]["email"] = "*****@*****.**"
db.__refero__()["users"]["user"]["metadata"]["soper"] = True
benchmarking.stop("modify user metadata")
print "registering two channels.."
benchmarking.start("reg two chans")
db.register_channel("#a", "password", "user")
db.register_channel("#b", "password", "user")
benchmarking.stop("reg two chans")
print "registering one channel.."
benchmarking.start("reg one chan")
db.register_channel("#c", "password", "user")
benchmarking.stop("reg one chan")
print "deregistering one channel.."
benchmarking.start("dereg one chan")
db.deregister_channel("#c")
benchmarking.stop("dereg one chan")
print "deregistering one user.."
benchmarking.start("dereg user")
db.deregister_user("user")
benchmarking.stop("dereg user")
print "synching database.."
benchmarking.start("sync db")
db.sync_db()
benchmarking.stop("sync db")
print "[INTENSE] registering 50,000 users.."
benchmarking.start("register 50000 users")
[db.register_user("%s" % (user), "password") for user in iusers]
benchmarking.stop("register 50000 users")
print "closing database.."
benchmarking.start("close db")
db.close_db()
benchmarking.stop("close db")
print "benchmarked."
f = open("benchmarks/results/database-results.txt", "w")
f.write(benchmarking.format_all())
f.close()
print "database benchmark is in benchmarks/results/database-results.txt"
os.system("rm etc/labere.db")
def get_psana_corrected_data(psana_det,
evt,
use_default=False,
dark=True,
common_mode=None,
apply_gain_mask=True,
gain_mask_value=None,
per_pixel_gain=False,
gain_mask=None,
additional_gain_factor=None):
"""
Given a psana Detector object, apply corrections as appropriate and return
the data from the event
@param psana_det psana Detector object
@param evt psana event
@param use_default If true, apply the default calibration only, using the
psana algorithms. Otherise, use the corrections specified by the rest of
the flags and values passed in.
@param dark Whether to apply the detector dark, bool or numpy array
@param common_mode Which common mode algorithm to apply. None: apply no
algorithm. Default: use the algorithm specified in the calib folder.
Otherwise should be a list as specified by the psana documentation for
common mode customization
@param apply_gain_mask Whether to apply the common mode gain mask correction
@param gain_mask_value Multiplier to apply to the pixels, according to the
gain mask
@param per_pixel_gain If available, use the per pixel gain deployed to the
calibration folder
@param gain_mask gain mask showing which pixels to apply gain mask value
@param additional_gain_factor Additional gain factor. Pixels counts are
divided by this number after all other corrections.
@return Numpy array corrected as specified.
"""
# order is pedestals, then common mode, then gain mask, then per pixel gain
# HACK: Force psana v2 behaviour
PSANA2_VERSION = True
start("psana_det.raw")
if PSANA2_VERSION:
# in psana2, data are stored as raw, fex, etc so the selection
# has to be given here when the detector interface is used.
# for now, assumes cctbx uses "raw".
psana_det = psana_det.raw
stop("psana_det.raw")
if use_default:
start("psana_det.calib")
ret = psana_det.calib(
evt) # applies psana's complex run-dependent calibrations
stop("psana_det.calib")
return ret
start("psana_det.raw_data(evt)")
data = psana_det.raw_data(evt)
stop("psana_det.raw_data(evt)")
if data is None:
return
start("subtract psana_det.pedestals()")
data = data.astype(np.float64)
if isinstance(dark, bool):
if dark:
if PSANA2_VERSION:
data -= psana_det.pedestals()
else:
data -= psana_det.pedestals(evt)
elif isinstance(dark, np.ndarray):
data -= dark
stop("subtract psana_det.pedestals()")
if common_mode is not None and common_mode != "default":
print("Applying common mode")
start("psana_det.common_mode_apply(data, common_mode)")
if common_mode == 'cspad_default':
common_mode = (1, 25, 25, 100, 1
) # default parameters for CSPAD images
psana_det.common_mode_apply(data, common_mode)
elif common_mode == 'unbonded':
common_mode = (5, 0, 0, 0, 0
) # unbonded pixels used for correction
psana_det.common_mode_apply(data, common_mode)
else: # this is how it was before.. Though I think common_mode would need to be a tuple..
psana_det.common_mode_apply(data, common_mode)
stop("psana_det.common_mode_apply(data, common_mode)")
else:
print("Not applying common mode")
if apply_gain_mask:
print("Applying gain mask")
start("apply gain mask")
if gain_mask is None: # TODO: consider try/except here
gain_mask = psana_det.gain_mask(evt) == 1
if gain_mask_value is None:
try:
gain_mask_value = psana_det._gain_mask_factor
except AttributeError:
print(
"No gain set for psana detector, using gain value of 1, consider disabling gain in your phil file"
)
gain_mask_value = 1
data[gain_mask] = data[gain_mask] * gain_mask_value
stop("apply gain mask")
else:
print("Not applying gain mask")
if per_pixel_gain: # TODO: test this
start("applying psana_det.gain()")
data *= psana_det.gain()
stop("applying psana_det.gain()")
if additional_gain_factor is not None:
data /= additional_gain_factor
return data
parser.add_argument(
"--of", help="Log dir -- every rank will write its own log file")
# Get args dict, and sanitize None types
args = vars(parser.parse_args())
output_name = args["of"]
del args["of"] # don't pass this to psana
psana_kwargs = set_defaults(args, default_parameters)
#
# Initialize MPI
#
start("INIT MPI")
from mpi4py import MPI
comm = MPI.COMM_WORLD
stop("INIT MPI")
rank = comm.Get_rank() # each process in MPI has a unique id, 0-indexed
#
# Run Benchmark
#
if rank == 0:
print("MPI Initialized, Running xtc_read Benchmark")
start(f"psana.DataSource({psana_kwargs})")
ds = psana.DataSource(**psana_kwargs)