def __init__(self, verbose=False, pidfile=None,
heartbeat_pvname=None,
pulsecount_pvname=None, **kws):
self.verbose = verbose
self.scandb = ScanDB()
try:
self.set_state(0)
except:
raise RuntimeError("Cannot connect to ScanDB")
self.state = 0
self.last = self.pulse = -1
self.last_move_time = 0
self.config = None
self.dead_time = 0.5
self.id_lookahead = 2
self.with_id = False
self.counters = []
self.pidfile = pidfile or DEFAULT_PIDFILE
self.pulsecount_pv = None
self.heartbeat_pv = None
if pulsecount_pvname is not None:
self.pulsecount_pv = PV(pulsecount_pvname)
if heartbeat_pvname is not None:
self.heartbeat_pv = PV(heartbeat_pvname)
self.connected = False
self.connect()
def __init__(self, suffix='h5', mask=None, **kws):
from epicsscan.scandb import ScanDB
self.scandb = ScanDB()
self.folder = ''
self.label = ''
self.mask = mask
self.suffix = suffix
self.sleep_time = 1.0
self.set_state('idle')
def __init__(self, **conn_kws):
self.scandb = ScanDB(**conn_kws)
self.state = 0
self.last = self.pulse = -1
self.last_move_time = 0
self.set_state(0)
self.config = None
self.dead_time = 1.1
self.connect()
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
self.scandb = ScanDB()
self.instdb = InstrumentDB(self.scandb)
print("Connect ScanDB ", self.scandb.engine, self.instname)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def connect_scandb(dbname=None, server='postgresql', _larch=None, **kwargs):
if (_larch.symtable.has_symbol(SCANDB_NAME)
and _larch.symtable.get_symbol(SCANDB_NAME) is not None):
scandb = _larch.symtable.get_symbol(SCANDB_NAME)
else:
scandb = ScanDB(dbname=dbname, server=server, **kwargs)
_larch.symtable.set_symbol(SCANDB_NAME, scandb)
if (_larch.symtable.has_symbol(INSTDB_NAME)
and _larch.symtable.get_symbol(INSTDB_NAME) is not None):
instdb = _larch.symtable.get_symbol(INSTDB_NAME)
else:
instdb = InstrumentDB(scandb)
_larch.symtable.set_symbol(INSTDB_NAME, instdb)
return scandb
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
dbconn_dir = dbconn.get('dbconn_dir', '')
dbconn_file = dbconn.get('dbconn_file', '')
if os.path.exists(dbconn_dir) and len(dbconn_file) > 0:
sys.path.insert(0, dbconn_dir)
mod = __import__(dbconn_file)
conn = mod.conn
scandb = ScanDB(**mod.conn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def connect_scandb(scandb=None, dbname=None, _larch=None, **kwargs):
global _scandb, _instdb
if _scandb is not None:
return _scandb
if scandb is None:
scandb = ScanDB(dbname=dbname, **kwargs)
if scandb is not None:
_scandb = scandb
if _larch is not None:
_larch.symtable.set_symbol(SCANDB_NAME, _scandb)
if _instdb is None:
_instdb = InstrumentDB(_scandb)
if _larch is not None:
_larch.symtable.set_symbol(INSTDB_NAME, _instdb)
return _scandb
class QXAFS_ScanWatcher(object):
def __init__(self, **conn_kws):
self.scandb = ScanDB(**conn_kws)
self.state = 0
self.last = self.pulse = -1
self.last_move_time = 0
self.set_state(0)
self.config = None
self.dead_time = 1.1
self.connect()
def connect(self):
self.config = json.loads(self.scandb.get_config('qxafs').notes)
pulse_channel = "%sCurrentChannel" % self.config['mcs_prefix']
self.pulse_pv = PV(pulse_channel, callback=self.onPulse)
self.idarray_pv = PV(self.config['id_array_pv'])
self.iddrive_pv = PV(self.config['id_drive_pv'])
self.idbusy_pv = PV(self.config['id_busy_pv'])
self.pulsecount_pv = PV(PULSECOUNT_PVNAME)
self.heartbeat_pv = PV(HEARTBEAT_PVNAME)
def qxafs_prep(self):
self.idarray = self.idarray_pv.get()
self.dtime = float(self.get_info(key='qxafs_dwelltime', default=0.5))
self.pulse = 0
self.last_move_time = 0
self.counters = []
for c in self.scandb.get_scandata():
pv = get_pv(c.pvname)
time.sleep(0.05)
for c in self.scandb.get_scandata():
pv = get_pv(c.pvname)
pv.connect()
self.counters.append((c.name, pv, pv.nelm))
def qxafs_finish(self):
nidarr = len(self.idarray)
self.idarray_pv.put(np.zeros(nidarr))
self.set_state(0)
self.dtime = 0.0
self.last, self.pulse = 0, 0
self.last_move_time = 0
self.counters = []
def onPulse(self, pvname, value=0, **kws):
self.pulse = value
def monitor_qxafs(self):
self.qxafs_prep()
print("Monitor QXAFS begin")
msg_counter = 0
last_pulse = 0
self.pulse = 0
while True:
if self.get_state() == 0:
print("Break : state=0")
break
npts = int(self.get_info(key='scan_total_points', default=0))
time.sleep(0.05)
now = time.time()
self.pulsecount_pv.put("%i" % self.pulse)
if self.pulse > last_pulse:
self.heartbeat_pv.put("%i" % int(time.time()))
val = self.idarray[self.pulse]
if (self.iddrive_pv.write_access and
(self.idbusy_pv.get() == 0) and
((now- self.last_move_time) > self.dead_time) and
(val > MIN_ID_ENERGY) and
(val < MAX_ID_ENERGY)):
try:
self.iddrive_pv.put(val)
self.last_move_time = time.time()
except:
pass
last_pulse = self.pulse
cpt = int(self.pulse)
time_left = (npts-cpt)*self.dtime
self.scandb.set_info('scan_time_estimate', time_left)
time_est = hms(time_left)
msg = 'Point %i/%i, time left: %s' % (cpt, npts, time_est)
if cpt >= 10*msg_counter:
self.scandb.set_info('scan_progress', msg)
msg_counter += 1
print(msg)
for name, pv, nelm in self.counters:
try:
if nelm > 1:
self.scandb.set_scandata(name, pv.get())
else:
buff = pv.get()
self.scandb.append_scandata(name, pv.get())
except:
print "Could not set scandata for %s: %i, %s" % (name, nelm, pv)
self.scandb.commit()
print("Monitor QXAFS done")
last_pulse = self.pulse = 0
self.qxafs_finish()
def get_info(self, *args, **kws):
return self.scandb.get_info(*args, **kws)
def set_state(self, val):
return self.scandb.set_info('qxafs_running', val)
def get_state(self):
return int(self.scandb.get_info(key='qxafs_running', default=0))
def mainloop(self):
while True:
if 1 == self.get_state():
self.monitor_qxafs()
time.sleep(1.0)
self.heartbeat_pv.put("%i"%int(time.time()))
class AD_Integrator(object):
"""1D integrator"""
def __init__(self, suffix='h5', mask=None, **kws):
from epicsscan.scandb import ScanDB
self.scandb = ScanDB()
self.folder = ''
self.label = ''
self.mask = mask
self.suffix = suffix
self.sleep_time = 1.0
self.set_state('idle')
def set_state(self, state):
self.scandb.set_info('xrd_1dint_status', state.lower())
def get_state(self):
return self.scandb.get_info('xrd_1dint_status').lower()
def read_config(self):
calfile = self.scandb.get_info('xrd_calibration')
self.label = self.scandb.get_info('xrd_1dint_label')
self.folder = self.scandb.get_info('map_folder')
if self.folder.endswith('/'):
self.folder = self.folder[:-1]
calib = json.loads(self.scandb.get_detectorconfig(calfile).text)
print("Read Integration configuration: ", calfile)
if HAS_PYFAI:
self.integrator = AzimuthalIntegrator(**calib)
def save_1dint(self, h5file, outfile):
t0 = time.time()
if not HAS_PYFAI:
return
try:
xrdfile = h5py.File(h5file, 'r')
except IOError:
time.sleep(2.0 * self.sleep_time)
return
data = xrdfile['/entry/data/data']
if self.mask is not None:
data = data * self.mask
if data.shape[1] > data.shape[2]:
data = data[:, 3:-3, 1:-1]
else:
data = data[:, 1:-1, 3:-3]
nframes, nx, ny = data.shape
xrdfile.close()
integrate = self.integrator.integrate1d
opts = dict(method='csr',
unit='q_A^-1',
correctSolidAngle=True,
polarization_factor=0.999)
dat = []
for i in range(nframes):
img = data[i, :, :]
img[np.where(img > MAXVAL)] = 0
q, x = integrate(img[::-1, :], 2048, **opts)
if i == 0:
dat.append(q)
dat.append(x)
dat = np.array(dat)
_path, fname = os.path.split(outfile)
print("writing 1D data: %s, %.2f sec" % (fname, time.time() - t0))
np.save(outfile, dat)
def integrate(self):
if len(self.folder) < 0:
self.read_config()
fname = '%s*.%s' % (self.label, self.suffix)
xrdfiles = glob.glob(os.path.join(self.folder, fname))
for xfile in sorted(xrdfiles):
outfile = xfile.replace(self.suffix, 'npy')
if not os.path.exists(outfile):
self.save_1dint(xfile, outfile)
def run(self):
while True:
time.sleep(self.sleep_time)
state = self.get_state()
# print(state, self.folder)
if state.startswith('starting'):
self.read_config()
self.set_state('running')
elif state.startswith('running'):
self.integrate()
elif state.startswith('finishing'):
self.integrate()
self.set_state('idle')
self.folder = ''
elif state.startswith('idle'):
time.sleep(5 * self.sleep_time)
elif state.startswith('quit'):
return
class QXAFS_ScanWatcher(object):
def __init__(self, verbose=False, pidfile=None,
heartbeat_pvname=None,
pulsecount_pvname=None, **kws):
self.verbose = verbose
self.scandb = ScanDB()
try:
self.set_state(0)
except:
raise RuntimeError("Cannot connect to ScanDB")
self.state = 0
self.last = self.pulse = -1
self.last_move_time = 0
self.config = None
self.dead_time = 0.5
self.id_lookahead = 2
self.with_id = False
self.counters = []
self.pidfile = pidfile or DEFAULT_PIDFILE
self.pulsecount_pv = None
self.heartbeat_pv = None
if pulsecount_pvname is not None:
self.pulsecount_pv = PV(pulsecount_pvname)
if heartbeat_pvname is not None:
self.heartbeat_pv = PV(heartbeat_pvname)
self.connected = False
self.connect()
def connect(self):
self.config = json.loads(self.scandb.get_config('qxafs').notes)
self.with_id = ('id_array_pv' in self.config and
'id_drive_pv' in self.config)
pulse_channel = "%sCurrentChannel" % self.config['mcs_prefix']
self.pulse_pv = PV(pulse_channel, callback=self.onPulse)
if self.with_id:
self.idarray_pv = PV(self.config['id_array_pv'])
self.iddrive_pv = PV(self.config['id_drive_pv'])
self.idbusy_pv = PV(self.config['id_busy_pv'])
pvroot = self.config['id_busy_pv'].replace('Busy', '')
self.idstop_pv = PV("%sStop" % pvroot)
self.idgapsym_pv = PV('%sGapSymmetry' % pvroot)
self.idtaper_pv = PV('%sTaperEnergy' % pvroot)
self.idtaperset_pv = PV('%sTaperEnergySet' % pvroot)
self.xps = NewportXPS(self.config['host'])
time.sleep(0.1)
self.connected = True
def qxafs_connect_counters(self):
self.counters = []
time.sleep(0.1)
pvs = []
for c in self.scandb.get_scandata():
pv = get_pv(c.pvname)
pvs.append((c.name, pv))
time.sleep(0.1)
for cname, pv in pvs:
pv.connect()
self.counters.append((cname, pv))
if self.verbose:
self.write("QXAFS_connect_counters %i counters" % (len(self.counters)))
def qxafs_finish(self):
nidarr = len(self.idarray)
# self.idarray_pv.put(np.zeros(nidarr))
self.set_state(0)
self.dtime = 0.0
self.last, self.pulse = 0, 0
self.last_move_time = 0
self.counters = []
def onPulse(self, pvname, value=0, **kws):
self.pulse = value
def monitor_qxafs(self):
msg_counter = 0
last_pulse = 0
self.pulse = 0
self.last_move_time = 0
if self.with_id:
self.idarray = self.idarray_pv.get()
else:
self.idarray = np.zeros(1)
self.dtime = float(self.scandb.get_info(key='qxafs_dwelltime', default=0.5))
if self.verbose:
self.write("Monitor QXAFS begin %i ID Points" % len(self.idarray))
self.qxafs_connect_counters()
while True:
if self.get_state() == 0:
print("Break : state=0")
break
npts = int(self.scandb.get_info(key='scan_total_points', default=0))
if self.scandb.get_info(key='request_abort', as_bool=True):
self.write("QXAFS scan aborted")
self.xps.abort_group()
time.sleep(1.0)
self.qxafs_finish()
break
time.sleep(0.05)
now = time.time()
# look for and prevent out-of-ordinary values for Taper (50 eV)
# or for Gap Symmetry
if self.with_id:
gapsym = self.idgapsym_pv.get()
taper = self.idtaper_pv.get()
if abs(gapsym) > 0.050 or abs(taper) > 0.050:
self.idtaperset_pv.put(0, wait=True)
time.sleep(0.250)
val = self.idarray[last_pulse + self.id_lookahead]
try:
self.iddrive_pv.put(val, wait=True, timeout=5.0)
except CASeverityException:
pass
time.sleep(0.250)
if self.pulse > last_pulse:
if self.pulsecount_pv is not None:
self.pulsecount_pv.put("%i" % self.pulse)
self.scandb.set_info('scan_current_point', self.pulse)
if self.heartbeat_pv is not None:
self.heartbeat_pv.put("%i" % int(time.time()))
# if the ID has been moving for more than 0.75 sec, stop it
if self.with_id:
if ((self.pulse > 2) and
(self.idbusy_pv.get() == 1) and
(now > self.last_move_time + 0.75)):
self.idstop_pv.put(1)
time.sleep(0.1)
val = self.idarray[self.pulse + self.id_lookahead]
if self.verbose and self.pulse % 25 == 0:
self.write("QXAFS: %d/%d ID Energy=%.3f " % (self.pulse, npts, val))
if ((self.idbusy_pv.get() == 0) and
(now > self.last_move_time + self.dead_time) and
(val > MIN_ID_ENERGY) and (val < MAX_ID_ENERGY)):
try:
self.iddrive_pv.put(val, wait=False)
except CASeverityException:
pass
time.sleep(0.1)
self.last_move_time = time.time()
else:
if self.verbose and self.pulse % 25 == 0:
self.write("QXAFS: %d/%d " % (self.pulse, npts))
last_pulse = self.pulse
cpt = int(self.pulse)
time_left = (npts-cpt)*self.dtime
self.scandb.set_info('scan_time_estimate', time_left)
time_est = hms(time_left)
msg = 'Point %i/%i, time left: %s' % (cpt, npts, time_est)
if cpt >= msg_counter:
self.scandb.set_info('scan_progress', msg)
self.scandb.set_info('heartbeat', tstamp())
msg_counter += 1
for name, pv in self.counters:
try:
value = pv.get()
if pv.nelm > 1:
self.scandb.set_scandata(name, value)
else:
self.scandb.append_scandata(name, value)
except:
self.write( "Could not set scandata for %s: %i, %s" % (name, pv))
self.scandb.commit()
if self.pulsecount_pv is not None:
self.pulsecount_pv.put("%i" % self.pulse)
self.scandb.set_info('scan_current_point', self.pulse)
self.write("Monitor QXAFS scan complete, finishing")
last_pulse = self.pulse = 0
self.qxafs_finish()
def set_state(self, val):
return self.scandb.set_info('qxafs_running', val)
def get_state(self):
val = self.scandb.get_info(key='qxafs_running', default=0)
return int(val)
def get_lastupdate(self):
if self.heartbeat_pv is not None:
return int(self.heartbeat_pv.get(as_string=True))
return -1
def kill_old_process(self):
print("kill old ", self.heartbeat_pv)
if self.heartbeat_pv is not None:
self.heartbeat_pv.put("-1")
pid = None
with open(self.pidfile) as fh:
pid = int(fh.readlines()[0][:-1])
if pid is not None:
self.write('killing pid=', pid, ' at ', time.ctime())
os.system("kill -9 %d" % pid)
time.sleep(1.0)
def save_pid(self):
with open(self.pidfile, 'w') as fh:
fh.write("%d\n" % os.getpid() )
fh.close()
def write(self, msg):
sys.stdout.write("%s\n" % msg)
sys.stdout.flush()
def mainloop(self):
if not self.connected:
self.connect()
self.save_pid()
self.qxafs_connect_counters()
while True:
state = self.get_state()
if 2 == int(state):
self.monitor_qxafs()
else:
if self.scandb.get_info(key='request_abort', as_bool=True):
self.xps.abort_group()
time.sleep(1.0)
time.sleep(1.0)
if self.heartbeat_pv is not None:
self.heartbeat_pv.put("%i"%int(time.time()))
self.write("QXAFS monitor mainloop done ")