def getCurrentHighTag(bl):
'''
returns current high tag value for current beamline
input: beamline
output: hightag value
'''
return dbpy.read_hightagnumber(bl, getNewestRun(bl))
def getHighTag(bl, run):
'''
returns high tag value for particular beamline and run number
input: beamline and runnumber as integers
output: high tag value as integer
'''
return dbpy.read_hightagnumber(bl, run)
def run(opts):
assert opts.runid is not None
assert opts.bl is not None
# Beamline specific constants
if opts.bl == 2:
sensor_spec = "xfel_bl_2_tc_spec_1/energy"
sensor_shutter = "xfel_bl_2_shutter_1_open_valid/status"
elif opts.bl == 3:
sensor_spec = "xfel_bl_3_tc_spec_1/energy"
sensor_shutter = "xfel_bl_3_shutter_1_open_valid/status"
else:
error_status("BadBeamline")
return -1
# Get run info
try:
run_info = dbpy.read_runinfo(opts.bl, opts.runid)
except:
error_status("BadRunID")
return -1
high_tag = dbpy.read_hightagnumber(opts.bl, opts.runid)
start_tag = run_info['start_tagnumber']
end_tag = run_info['end_tagnumber']
tag_list = numpy.array(dbpy.read_taglist_byrun(opts.bl, opts.runid))
print "# Run %d: HighTag %d, Tags %d (inclusive) to %d (exclusive), thus %d tags" % (opts.runid, high_tag, start_tag, end_tag, len(tag_list))
comment = dbpy.read_comment(opts.bl, opts.runid)
print "# Comment: %s" % comment
# Get shutter status and find images
try:
shutter = numpy.array(map(str2float, dbpy.read_syncdatalist(sensor_shutter, high_tag, tuple(tag_list))))
except:
print traceback.format_exc()
error_status("NoShutterStatus")
return -1
# XXX
valid_tags = tag_list[shutter==1] # [tag for tag, is_open in zip(tag_list, shutter) if is_open == 1]
if 0:
tag_offset = 3
tag_list = tag_list[tag_offset:]
valid_tags = tag_list[numpy.arange(1, len(tag_list)+1)%6==0]
if valid_tags.size == 0:
error_status("NoValidTags")
return -1
# Get PD values
pd1_values, pd2_values, pd3_values = map(lambda y: map(lambda x: float("nan"), xrange(len(valid_tags))), xrange(3))
if opts.pd1_sensor_name:
pd1_values = numpy.array(map(str2float, dbpy.read_syncdatalist(opts.pd1_sensor_name, high_tag, tuple(valid_tags))))
if opts.pd2_sensor_name:
pd2_values = numpy.array(map(str2float, dbpy.read_syncdatalist(opts.pd2_sensor_name, high_tag, tuple(valid_tags))))
if opts.pd3_sensor_name:
pd3_values = numpy.array(map(str2float, dbpy.read_syncdatalist(opts.pd3_sensor_name, high_tag, tuple(valid_tags))))
print "tag pd1 pd2 pd3"
for tag, pd1, pd2, pd3 in zip(valid_tags, pd1_values, pd2_values, pd3_values):
print tag, pd1, pd2, pd3
for i in xrange(len(valid_tags)):
bad = []
if (opts.pd1_threshold != 0 and
not (opts.pd1_threshold > 0 and opts.pd1_threshold <= pd1_values[i]) and
not (opts.pd1_threshold < 0 and -opts.pd1_threshold > pd1_values[i])): bad.append(1)
if (opts.pd2_threshold != 0 and
not (opts.pd2_threshold > 0 and opts.pd2_threshold <= pd2_values[i]) and
not (opts.pd2_threshold < 0 and -opts.pd2_threshold > pd2_values[i])): bad.append(2)
if (opts.pd3_threshold != 0 and
not (opts.pd3_threshold > 0 and opts.pd3_threshold <= pd3_values[i]) and
not (opts.pd3_threshold < 0 and -opts.pd3_threshold > pd3_values[i])): bad.append(3)
if bad:
print "# Bad tag=%d BadPD=%s" %(valid_tags[i], bad)
def run(opts):
eltime_from = time.time()
print("#\n#Configurations:")
print("# runNumber (-r/--run): %d" % opts.runid)
print("# output H5 file (-o/--output): %s (default = run######.h5)" %
opts.outputH5)
print("# beamline (--bl): %d (default = 3)" % opts.bl)
print("# img root (--rayonix-root): %s" % opts.rayonix_root)
print("# distance (--clen): %s" % opts.clen)
print("# beam center (--beam-x/y): %s,%s" % (opts.beam_x, opts.beam_y))
print("# Cheetah settings")
print("# --dmin, --dmax: %s,%s" % (opts.d_min, opts.d_max))
print("# --adc-threshold: %s" % opts.ADCthresh)
print("# --min-snr: %s" % opts.MinSNR)
print("# --min/max-pixcount: %s,%s" %
(opts.MinPixCount, opts.MaxPixCount))
print("# --local-bgradius: %s" % opts.LocalBGRadius)
print("# --min-peaksep: %s" % opts.MinPeakSeparation)
print("# --min-spots: %s" % opts.min_spots)
print("# --algorithm: %s" % opts.algorithm)
print("# PD1 threshold (--pd1_thresh): %.3f (default = 0; ignore.)" %
opts.pd1_threshold)
print("# PD2 threshold (--pd2_thresh): %.3f (default = 0; ignore.)" %
opts.pd2_threshold)
print("# PD3 threshold (--pd3_thresh): %.3f (default = 0; ignore.)" %
opts.pd3_threshold)
print("# PD1 sensor name (--pd1_name): %s)" % opts.pd1_sensor_name)
print("# PD2 sensor name (--pd2_name): %s)" % opts.pd2_sensor_name)
print("# PD3 sensor name (--pd3_name): %s)" % opts.pd3_sensor_name)
print(
"# nFrame after light: %d (default = -1; accept all image. -2; accept all dark images)"
% opts.light_dark)
print(
"# parallel_block: %d (default = -1; no parallelization)"
% opts.parallel_block)
print("# nproc: %d (default = 1)" % opts.nproc)
print("")
assert opts.algorithm in (6, 8)
assert opts.runid is not None
assert opts.bl is not None
# Beamline specific constants
if opts.bl == 2:
sensor_spec = "xfel_bl_2_tc_spec_1/energy"
sensor_shutter = "xfel_bl_2_shutter_1_open_valid/status"
elif opts.bl == 3:
sensor_spec = "xfel_bl_3_tc_spec_1/energy"
sensor_shutter = "xfel_bl_3_shutter_1_open_valid/status"
else:
error_status("BadBeamline")
return -1
# Get run info
try:
run_info = dbpy.read_runinfo(opts.bl, opts.runid)
except:
error_status("BadRunID")
return -1
high_tag = dbpy.read_hightagnumber(opts.bl, opts.runid)
start_tag = run_info['start_tagnumber']
end_tag = run_info['end_tagnumber']
tag_list = numpy.array(dbpy.read_taglist_byrun(opts.bl, opts.runid))
print "# Run %d: HighTag %d, Tags %d (inclusive) to %d (exclusive), thus %d tags" % (
opts.runid, high_tag, start_tag, end_tag, len(tag_list))
comment = dbpy.read_comment(opts.bl, opts.runid)
print "# Comment: %s" % comment
print
# Get shutter status and find images
try:
shutter = numpy.array(
map(
str2float,
dbpy.read_syncdatalist(sensor_shutter, high_tag,
tuple(tag_list))))
except:
print traceback.format_exc()
error_status("NoShutterStatus")
return -1
# XXX
valid_tags = tag_list[
shutter ==
1] # [tag for tag, is_open in zip(tag_list, shutter) if is_open == 1]
print "# DEBUG:: shutter=", shutter
print "# DEBUG:: valid_tags=", valid_tags
if 0:
tag_offset = 3
tag_list = tag_list[tag_offset:]
valid_tags = tag_list[numpy.arange(1, len(tag_list) + 1) % 6 == 0]
if valid_tags.size == 0:
error_status("NoValidTags")
return -1
# Find images
img_files = sorted(
glob.glob(
os.path.join(opts.rayonix_root, str(opts.runid), "data_*.img")))
print "# DEBUG:: img_files=%d valid_tags=%d" % (len(img_files),
len(valid_tags))
if len(img_files) + 1 != len(valid_tags): # last valid tag is not saved.
print "# WARNING!! img_files and valid_tag number mismatch"
img_numbers = map(lambda x: int(x[x.rindex("_") + 1:-4]), img_files)
dropped_frames = sorted(
set(range(1, len(valid_tags))).difference(img_numbers))
print "# Unsaved frame numbers =", tuple(dropped_frames)
print "# DEBUG::", len(img_files) - len(dropped_frames) + 1, len(
valid_tags)
if len(img_files) + len(dropped_frames) + 1 == len(valid_tags):
print "# %d unsaved img files found, which explains number mismatch" % len(
dropped_frames)
valid_tags = numpy.delete(valid_tags,
numpy.array(dropped_frames) - 1)
assert len(img_files) + 1 == len(valid_tags)
else:
print "# Assuming last %d img files are generated after stopping run.." % (
len(img_files) - len(valid_tags) + 1)
img_files = img_files[:len(valid_tags) - 1]
assert len(img_files) + 1 == len(valid_tags)
# Get photon energies
photon_energies_in_keV = numpy.array([
str2float(s) for s in dbpy.read_syncdatalist(sensor_spec, high_tag,
tuple(valid_tags))
])
mean_photon_energy = numpy.mean(photon_energies_in_keV[
photon_energies_in_keV ==
photon_energies_in_keV]) # XXX if no valid data?
print "# Photon energies obtained: %d valid numbers, %d invalid, average=%f sd=%f" % (
len(photon_energies_in_keV),
sum(photon_energies_in_keV != photon_energies_in_keV),
mean_photon_energy,
numpy.std(photon_energies_in_keV[photon_energies_in_keV ==
photon_energies_in_keV]))
photon_energies_in_keV[
photon_energies_in_keV != photon_energies_in_keV] = mean_photon_energy
# Get PD values
pd1_values, pd2_values, pd3_values = [], [], []
if opts.pd1_threshold != 0:
pd1_values = numpy.array(
map(
str2float,
dbpy.read_syncdatalist(opts.pd1_sensor_name, high_tag,
tuple(valid_tags))))
if opts.pd2_threshold != 0:
pd2_values = numpy.array(
map(
str2float,
dbpy.read_syncdatalist(opts.pd2_sensor_name, high_tag,
tuple(valid_tags))))
if opts.pd3_threshold != 0:
pd3_values = numpy.array(
map(
str2float,
dbpy.read_syncdatalist(opts.pd3_sensor_name, high_tag,
tuple(valid_tags))))
# Identify bad tags
# XXX not tested!! this feature must not be used. tags with bad PDs must be detected after experiment.
frame_after_light = 9999
bad_tag_idxes = []
for i in xrange(len(valid_tags)):
light = True
if (opts.pd1_threshold != 0
and not (opts.pd1_threshold > 0
and opts.pd1_threshold <= pd1_values[i])
and not (opts.pd1_threshold < 0
and -opts.pd1_threshold > pd1_values[i])):
light = False
if (opts.pd2_threshold != 0
and not (opts.pd2_threshold > 0
and opts.pd2_threshold <= pd2_values[i])
and not (opts.pd2_threshold < 0
and -opts.pd2_threshold > pd2_values[i])):
light = False
if (opts.pd3_threshold != 0
and not (opts.pd3_threshold > 0
and opts.pd3_threshold <= pd3_values[i])
and not (opts.pd3_threshold < 0
and -opts.pd3_threshold > pd3_values[i])):
light = False
if light:
frame_after_light = 0
else:
frame_after_light += 1
if ((opts.light_dark >= 0 and frame_after_light != opts.light_dark) or
(opts.light_dark == PD_DARK_ANY and frame_after_light == 0)):
print "# PD check: %d is bad tag!" % valid_tags[i]
bad_tag_idxes.append(i)
if bad_tag_idxes:
valid_tags = numpy.delete(valid_tags, numpy.array(bad_tag_idxes))
for i in reversed(bad_tag_idxes):
del img_files[i]
# Debug code; this takes too much time!
try:
if 0 and opts.parallel_block == 0:
tag_timestamp = map(
lambda x: datetime.datetime.fromtimestamp(
dbpy.read_timestamp_fromtag(high_tag, x, sensor_shutter)).
strftime('%Y-%m-%d %H:%M:%S.%f'), valid_tags)
img_timestamp = map(
lambda x: marccd.MarCCD(x).acquire_time.strftime(
'%Y-%m-%d %H:%M:%S.%f'), img_files)
ofs = open("tag_file_time.dat", "w")
ofs.write("run tag file tag.time file.time\n")
for i in xrange(len(img_files)):
ofs.write('%d %d %s "%s" "%s"\n' %
(opts.runid, valid_tags[i], img_files[i],
tag_timestamp[i], img_timestamp[i]))
ofs.close()
except:
pass
# block spliting
# TODO db query may be slow, which may need to be done only once?
if opts.parallel_block >= 0:
width = len(valid_tags) // parallel_size
i_start = opts.parallel_block * width
i_end = (opts.parallel_block + 1
) * width if opts.parallel_block < parallel_size - 1 else None
valid_tags = valid_tags[i_start:i_end]
photon_energies_in_keV = photon_energies_in_keV[i_start:i_end]
img_files = img_files[i_start:i_end]
print "# parallel_block=%d: %d tags will be processed (%d..%d)" % (
opts.parallel_block, len(valid_tags), valid_tags[0],
valid_tags[-1])
make_geom(img_files[0],
opts.output_geom,
beam_x=opts.beam_x,
beam_y=opts.beam_y,
clen=opts.clen)
# Hit-finding
results = process_images(img_files, mean_photon_energy, opts)
file_tag_ene = []
for frame, tag, ene in zip(sorted(results), valid_tags,
photon_energies_in_keV):
if len(results[frame]["spots"]) < opts.min_spots:
continue
file_tag_ene.append((frame, tag, ene))
# TODO on-the-fly status updating
open("status.txt", "w").write("""\
# Cheetah status
Update time: %(ctime)s
Elapsed time: %(eltime)f sec
Status: Total=%(ntotal)d,Processed=%(ntotal)d,LLFpassed=%(ntotal)d,Hits=%(nhits)d,Status=WritingH5
Frames processed: %(ntotal)d
Number of hits: %(nhits)d
""" % dict(ctime=time.ctime(),
eltime=time.time() - eltime_from,
ntotal=len(img_files),
nhits=len(file_tag_ene)))
# Save h5
# TODO implement on-the-fly h5 file writing in hit-finding to avoid reading img file twice.
make_h5(out=opts.outputH5, file_tag_ene=file_tag_ene, comment=comment)
open("status.txt", "w").write("""\
# Cheetah status
Update time: %(ctime)s
Elapsed time: %(eltime)f sec
Status: Total=%(ntotal)d,Processed=%(ntotal)d,LLFpassed=%(ntotal)d,Hits=%(nhits)d,Status=Finished
Frames processed: %(ntotal)d
Number of hits: %(nhits)d
""" % dict(ctime=time.ctime(),
eltime=time.time() - eltime_from,
ntotal=len(img_files),
nhits=len(file_tag_ene)))
ofs = open("cheetah.dat", "w")
ofs.write("file tag nspots total_snr\n")
for frame, tag in zip(sorted(results), valid_tags):
ret = results[frame]
n_spots = len(ret["spots"])
total_snr = sum(map(lambda x: x[2], ret["spots"]))
ofs.write("%s %d %6d %.3e\n" % (frame, tag, n_spots, total_snr))
ofs.close()
if opts.gen_adx:
for frame in sorted(results):
ret = results[frame]
adx_out = open(os.path.basename(frame) + ".adx", "w")
for x, y, snr, d in ret["spots"]:
adx_out.write("%6d %6d %.2e\n" % (x, y, snr))
adx_out.close()
def run(runid, bl=3, clen=50.0):
# Beamline specific constants
if bl == 2:
sensor_spec = "xfel_bl_2_tc_spec_1/energy"
sensor_shutter = "xfel_bl_2_shutter_1_open_valid/status"
elif bl == 3:
sensor_spec = "xfel_bl_3_tc_spec_1/energy"
sensor_shutter = "xfel_bl_3_shutter_1_open_valid/status"
else:
log_error("BadBeamline")
sys.exit(-1)
# Get Run info
try:
run_info = dbpy.read_runinfo(bl, runid)
except:
log_error("BadRunID")
sys.exit(-1)
high_tag = dbpy.read_hightagnumber(bl, runid)
start_tag = run_info['start_tagnumber']
end_tag = run_info['end_tagnumber']
tag_list = dbpy.read_taglist_byrun(bl, runid)
tag = tag_list[0]
print "Run %d: HighTag %d, Tags %d (inclusive) to %d (exclusive), thus %d images" % (
runid, high_tag, start_tag, end_tag, len(tag_list))
comment = dbpy.read_comment(bl, runid)
print "Comment: %s" % comment
print
# Find detectors
det_IDs = dbpy.read_detidlist(bl, runid)
print "Detector IDs: " + " ".join(det_IDs)
det_IDs = sorted([x for x in det_IDs if re.match("^MPCCD-8.*-[1-8]$", x)])
if len(det_IDs) != 8:
log_error("NoSupportedDetectorFound")
sys.exit(-1)
print "MPCCD Octal IDs to use: " + " ".join(det_IDs)
print
# Get shutter status and find dark images
try:
shutter = [
str2float(s)
for s in dbpy.read_syncdatalist(sensor_shutter, high_tag, tag_list)
]
except:
log_error("NoShutterStatus")
sys.exit(-1)
dark_tags = [
tag for tag, is_open in zip(tag_list, shutter) if is_open == 0
]
if bl == 2 and runid >= 32348: # and runid <= 33416:
# 2018 Feb: Unreliable shutter status. Should use PD and take darks only at the beginning of a run
print "The shutter status was unreliable for runs in 2018 Feb."
print "The number of tags with shutter closed:", len(dark_tags)
print "Since the above value is not reliable, we use X-ray PD values instead."
xray_pd = "xfel_bl_2_st_3_bm_1_pd/charge"
pd_values = [
str2float(s)
for s in dbpy.read_syncdatalist(xray_pd, high_tag, tag_list)
]
dark_tags = []
is_head = True
for tag, pd in zip(tag_list, pd_values):
if pd == None and is_head:
dark_tags.append(tag)
else:
is_head = False
print "Number of tags without X-ray:", len(
[1 for pd_val in pd_values if pd_val is None])
print "But we use only tags at the beginning of a run."
if len(dark_tags) == 0:
log_error("NoDarkImage")
sys.exit(-1)
print "Number of dark images to average: %d" % len(dark_tags)
print
# Setup buffer readers
try:
readers = [
stpy.StorageReader(det_id, bl, (runid, )) for det_id in det_IDs
]
except:
log_error("FailedOn_create_streader")
sys.exit(-1)
try:
buffers = [stpy.StorageBuffer(reader) for reader in readers]
except:
log_error("FailedOn_create_stbuf")
sys.exit(-1)
# Read first image to get detector info
det_infos = []
for reader, buf in zip(readers, buffers):
try:
reader.collect(buf, dark_tags[0])
except:
log_error("FailedOn_collect_data")
sys.exit(-1)
det_infos = [buf.read_det_info(0) for buf in buffers]
for i, det_info in enumerate(det_infos):
det_info['id'] = det_IDs[i]
# Collect pulse energies
config_photon_energy = 1000.0 * dbpy.read_config_photonenergy(bl, runid)
config_photon_energy_sensible = True
if config_photon_energy < 5000 or config_photon_energy > 14000:
print "WARNING: dbpy.read_config_photonenergy returned %f eV, which is absurd!" % config_photon_energy
print " Report this to SACLA DAQ team."
print " This is not problematic unless the inline spectrometer is also broken."
config_photon_energy_sensible = False
pulse_energies_in_keV = [
str2float(s) for s in dbpy.read_syncdatalist(sensor_spec, high_tag,
tuple(dark_tags))
]
pulse_energies = []
for tag, energy in zip(dark_tags, pulse_energies_in_keV):
if energy is not None and energy > 0:
pulse_energies.append(energy * 1000.0)
else:
print "WARNING: The wavelength from the inline spectrometer does not look sensible for tag %d." % tag
if config_photon_energy_sensible:
pulse_energies.append(config_photon_energy)
print " Used the accelerator config value instead."
else:
pulse_energies.append(7000.0)
print " The accelerator config value is also broken; assumed 7 keV as a last resort!"
print
mean_energy = np.mean(pulse_energies)
print "Mean photon energy: %f eV" % mean_energy
print "Configured photon energy: %f eV" % config_photon_energy
print
# Create geometry files
write_crystfel_geom("%d.geom" % runid, det_infos, mean_energy, clen)
write_cheetah_geom("%d-geom.h5" % runid, det_infos)
# Write metadata
write_metadata("%d.h5" % runid, det_infos, clen, comment)
# Create dark average
print
print "Calculating a dark average:"
num_added = 0
sum_buffer = np.zeros((YSIZE * NPANELS, XSIZE), dtype=np.float64)
gains = [det_info['mp_absgain'] for det_info in det_infos]
for j, tag_id in enumerate(dark_tags):
print "Processing tag %d (%2.1f%% done)" % (tag_id, 100.0 *
(j + 1) / len(dark_tags))
if (j % 5 == 0):
with open("status.txt", "w") as status:
status.write(
"Status: Total=%d,Processed=%d,Status=DarkAveraging\n" %
(len(dark_tags), j + 1))
num_added += add_image(sum_buffer, readers, buffers, gains, tag_id,
pulse_energies[j])
print "\nDone. Averaged %d frames." % num_added
if (num_added < 1):
return -1
sum_buffer /= num_added
ushort_max = np.iinfo(np.uint16).max
print " #neg (< 0) %d, #overflow (> %d) %d" % (np.sum(
sum_buffer < 0), ushort_max, np.sum(sum_buffer > ushort_max))
sum_buffer[sum_buffer < 0] = 0
sum_buffer[sum_buffer > ushort_max] = ushort_max
averaged = sum_buffer.astype(np.uint16)
# In the Phase 3 detector, some pixels average to negative values.
# Most are around -0.1 and all those below -1 are at panel edges that will be masked.
# So we don't have to worry about them.
f = h5py.File("%d-dark.h5" % runid, "w")
f.create_dataset("/data/data",
data=averaged,
compression="gzip",
shuffle=True)
# f.create_dataset("/data/raw", data=sum_buffer, compression="gzip", shuffle=True)
f.close()
print "Dark average was written to %s" % ("%d-dark.h5" % runid)
def run(runid, bl=3, clen=50.0, dry_run=False):
# Beamline specific constants
if bl == 2:
sensor_spec = "xfel_bl_2_tc_spec_1/energy"
sensor_shutter = "xfel_bl_2_shutter_1_open_valid/status"
elif bl == 3:
sensor_spec = "xfel_bl_3_tc_spec_1/energy"
sensor_shutter = "xfel_bl_3_shutter_1_open_valid/status"
else:
log_error("BadBeamline")
sys.exit(-1)
# Get Run info
try:
run_info = dbpy.read_runinfo(bl, runid)
except:
log_error("BadRunID")
sys.exit(-1)
high_tag = dbpy.read_hightagnumber(bl, runid)
start_tag = run_info['start_tagnumber']
end_tag = run_info['end_tagnumber']
tag_list = dbpy.read_taglist_byrun(bl, runid)
tag = tag_list[0]
print "Run %d: HighTag %d, Tags %d (inclusive) to %d (exclusive), thus %d images" % (runid, high_tag, start_tag, end_tag, len(tag_list))
comment = dbpy.read_comment(bl, runid)
print "Comment: %s" % comment
print
# Find detectors
det_IDs = dbpy.read_detidlist(bl, runid)
print "Detector IDs: " + " ".join(det_IDs)
det_IDs = sorted([x for x in det_IDs if re.match("^MPCCD-8.*-[1-8]$", x)])
if len(det_IDs) != 8:
log_error("NoSupportedDetectorFound")
sys.exit(-1)
print "MPCCD Octal IDs to use: " + " ".join(det_IDs)
print
# Get shutter status and find dark images
try:
shutter = [str2float(s) for s in dbpy.read_syncdatalist(sensor_shutter, high_tag, tag_list)]
except:
log_error("NoShutterStatus")
sys.exit(-1)
dark_tags = [tag for tag, is_open in zip(tag_list, shutter) if is_open == 0]
if bl == 2 and runid >= 32348: # and runid <= 33416:
# 2018 Feb: Unreliable shutter status. We should use BM1 PD and take darks only at the beginning of a run
print "The shutter status was unreliable for runs since 2018 Feb."
print "The number of tags with shutter closed:", len(dark_tags)
print "Since the above value is not reliable, we use X-ray PD values instead."
xray_pd = "xfel_bl_2_st_3_bm_1_pd/charge"
pd_values = [str2float(s) for s in dbpy.read_syncdatalist(xray_pd, high_tag, tag_list)]
dark_tags = []
is_head = True
for tag, pd in zip(tag_list, pd_values):
if math.isnan(pd) and is_head:
dark_tags.append(tag)
else:
is_head = False
print "Number of tags without X-ray:", len([1 for pd_val in pd_values if math.isnan(pd_val)])
print "But we use only tags at the beginning of a run."
if len(dark_tags) == 0:
log_error("NoDarkImage")
sys.exit(-1)
print "Number of dark images to average: %d" % len(dark_tags)
print
# Setup buffer readers
try:
readers = [stpy.StorageReader(det_id, bl, (runid,)) for det_id in det_IDs]
except:
log_error("FailedOn_create_streader")
sys.exit(-1)
try:
buffers = [stpy.StorageBuffer(reader) for reader in readers]
except:
log_error("FailedOn_create_stbuf")
sys.exit(-1)
# Read first image to get detector info
det_infos = []
for reader, buf in zip(readers, buffers):
try:
reader.collect(buf, dark_tags[0])
except:
log_error("FailedOn_collect_data")
sys.exit(-1)
det_infos = [buf.read_det_info(0) for buf in buffers]
for i, det_info in enumerate(det_infos):
det_info['id'] = det_IDs[i]
# Collect pulse energies
config_photon_energy = 1000.0 * dbpy.read_config_photonenergy(bl, runid)
config_photon_energy_sensible = True
if config_photon_energy < 5000 or config_photon_energy > 14000:
print "WARNING: dbpy.read_config_photonenergy returned %f eV, which is absurd!" % config_photon_energy
print " Report this to SACLA DAQ team."
print " This is not problematic unless the inline spectrometer is also broken."
config_photon_energy_sensible = False
pulse_energies_in_keV = [str2float(s) for s in dbpy.read_syncdatalist(sensor_spec, high_tag, tuple(dark_tags))]
pulse_energies = []
for tag, energy in zip(dark_tags, pulse_energies_in_keV):
if energy is not None and energy > 0:
pulse_energies.append(energy * 1000.0)
else:
print "WARNING: The wavelength from the inline spectrometer does not look sensible for tag %d." % tag
if config_photon_energy_sensible:
pulse_energies.append(config_photon_energy)
print " Used the accelerator config value instead."
else:
pulse_energies.append(7000.0)
print " The accelerator config value is also broken; assumed 7 keV as a last resort!"
print
mean_energy = np.mean(pulse_energies)
print "Mean photon energy: %f eV" % mean_energy
print "Configured photon energy: %f eV" % config_photon_energy
print
# Create geometry files
write_crystfel_geom("%d.geom" % runid, det_infos, mean_energy, clen)
write_cheetah_geom("%d-geom.h5" % runid, det_infos)
# Write metadata
write_metadata("%d.h5" % runid, det_infos, clen, comment)
if (dry_run): return
# Create dark average
print
print "Calculating a dark average:"
num_added = 0
sum_buffer = np.zeros((YSIZE * NPANELS, XSIZE), dtype=np.float64)
gains = [det_info['mp_absgain'] for det_info in det_infos]
for j, tag_id in enumerate(dark_tags):
print "Processing tag %d (%2.1f%% done)" % (tag_id, 100.0 * (j + 1) / len(dark_tags))
if (j % 5 == 0):
with open("status.txt", "w") as status:
status.write("Status: Total=%d,Processed=%d,Status=DarkAveraging\n" % (len(dark_tags), j + 1))
num_added += add_image(sum_buffer, readers, buffers, gains, tag_id, pulse_energies[j])
print "\nDone. Averaged %d frames." % num_added
if (num_added < 1):
return -1
sum_buffer /= num_added
ushort_max = np.iinfo(np.uint16).max
print " #neg (< 0) %d, #overflow (> %d) %d" % (np.sum(sum_buffer < 0), ushort_max, np.sum(sum_buffer > ushort_max))
sum_buffer[sum_buffer < 0] = 0
sum_buffer[sum_buffer > ushort_max] = ushort_max
averaged = sum_buffer.astype(np.uint16)
# In the Phase 3 detector, some pixels average to negative values.
# Most are around -0.1 and all those below -1 are at panel edges that will be masked.
# So we don't have to worry about them.
f = h5py.File("%d-dark.h5" % runid, "w")
f.create_dataset("/data/data", data=averaged, compression="gzip", shuffle=True)
# f.create_dataset("/data/raw", data=sum_buffer, compression="gzip", shuffle=True)
f.close()
print "Dark average was written to %s" % ("%d-dark.h5" % runid)
def getCurrentHighTag(bl):
return dbpy.read_hightagnumber(bl, getNewestRun(bl))
def getHighTag(bl, run):
return dbpy.read_hightagnumber(bl, run)
def run(opts):
eltime_from = time.time()
assert opts.runid is not None
assert opts.bl is not None
# Beamline specific constants
if opts.bl == 2:
sensor_spec = "xfel_bl_2_tc_spec_1/energy"
sensor_shutter = "xfel_bl_2_shutter_1_open_valid/status"
elif opts.bl == 3:
sensor_spec = "xfel_bl_3_tc_spec_1/energy"
sensor_shutter = "xfel_bl_3_shutter_1_open_valid/status"
else:
error_status("BadBeamline")
return -1
# Get run info
try:
run_info = dbpy.read_runinfo(opts.bl, opts.runid)
except:
error_status("BadRunID")
return -1
high_tag = dbpy.read_hightagnumber(opts.bl, opts.runid)
start_tag = run_info['start_tagnumber']
end_tag = run_info['end_tagnumber']
tag_list = numpy.array(dbpy.read_taglist_byrun(opts.bl, opts.runid))
print "# Run %d: HighTag %d, Tags %d (inclusive) to %d (exclusive), thus %d images" % (opts.runid, high_tag, start_tag, end_tag, len(tag_list))
comment = dbpy.read_comment(opts.bl, opts.runid)
print "# Comment: %s" % comment
print
# Get shutter status and find images
try:
shutter = numpy.array(map(str2float, dbpy.read_syncdatalist(sensor_shutter, high_tag, tuple(tag_list))))
except:
print traceback.format_exc()
error_status("NoShutterStatus")
return -1
# XXX
valid_tags = tag_list[shutter==1] # [tag for tag, is_open in zip(tag_list, shutter) if is_open == 1]
print "DEBUG:: shutter=", shutter
print "DEBUG:: valid_tags=", valid_tags
if 0:
tag_offset = 3
tag_list = tag_list[tag_offset:]
valid_tags = tag_list[numpy.arange(1, len(tag_list)+1)%6==0]
if valid_tags.size == 0:
error_status("NoValidTags")
return -1
# Find images
img_files = sorted(glob.glob(os.path.join(opts.rayonix_root, str(opts.runid), "data_*.img")))
print "# DEBUG:: img_files=%d valid_tags=%d" % (len(img_files), len(valid_tags))
if len(img_files)+1 != len(valid_tags): # last valid tag is not saved.
print "# WARNING!! img_files and valid_tag number mismatch"
img_numbers = map(lambda x: int(x[x.rindex("_")+1:-4]), img_files)
dropped_frames = sorted(set(range(1, len(valid_tags))).difference(img_numbers))
print "# Unsaved frame numbers =", tuple(dropped_frames)
print "# DEBUG::", len(img_files)-len(dropped_frames)+1, len(valid_tags)
if len(img_files)+len(dropped_frames)+1 == len(valid_tags):
print "# %d unsaved img files found, which explains number mismatch" % len(dropped_frames)
valid_tags = numpy.delete(valid_tags, numpy.array(dropped_frames)-1)
assert len(img_files)+1 == len(valid_tags)
else:
print "# Assuming last %d img files are generated after stopping run.." % (len(img_files)-len(valid_tags)+1)
img_files = img_files[:len(valid_tags)-1]
assert len(img_files)+1 == len(valid_tags)
tag_timestamp = map(lambda x: datetime.datetime.fromtimestamp(dbpy.read_timestamp_fromtag(high_tag, x, sensor_shutter)).strftime('%Y-%m-%d %H:%M:%S.%f'), valid_tags)
img_timestamp = map(lambda x: marccd.MarCCD(x).acquire_time.strftime('%Y-%m-%d %H:%M:%S.%f'), img_files)
ofs = open("tag_file_time.dat", "w")
ofs.write("run tag file tag.time file.time\n")
for i in xrange(len(img_files)):
ofs.write('%d %d %s "%s" "%s"\n'%(opts.runid, valid_tags[i], img_files[i], tag_timestamp[i], img_timestamp[i]))
ofs.close()