def __init__(self, xrf_prefix='13SDD1:', configfile=None):
self._pvs = {}
self.state = 'idle'
self.xmap = None
self.xsp3 = None
self.xrdcam = None
conf = self.mapconf = FastMapConfig(configfile)
print(" Using Configfile : ", configfile)
struck = conf.get('general', 'struck')
scaler = conf.get('general', 'scaler')
basedir = conf.get('general', 'basedir')
mapdb = conf.get('general', 'mapdb')
self.use_xrd = conf.get('xrd_ad', 'use')
self.use_xrf = conf.get('xrf', 'use')
self.xrf_type = conf.get('xrf', 'type')
self.xrf_pref = conf.get('xrf', 'prefix')
self.mapper = mapper(prefix=mapdb)
self.scan_t0 = time.time()
self.Connect_ENV_PVs()
self.ROI_Written = False
self.ENV_Written = False
self.ROWS_Written = False
self.xps = XPSTrajectory(**conf.get('xps'))
self.dtime = debugtime()
self.struck = Struck(struck, scaler=scaler)
self.struck.read_all_mcas()
print 'Using xrf type/prefix= ', self.xrf_type, self.xrf_pref
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap = MultiXMAP(self.xrf_pref)
elif self.xrf_type.startswith('xsp'):
self.xsp3 = Xspress3(self.xrf_pref, fileroot='/T/')
if self.use_xrd:
filesaver = conf.get('xrd_ad', 'fileplugin')
prefix = conf.get('xrd_ad', 'prefix')
xrd_type = conf.get('xrd_ad', 'type')
print(" Use XRD ", prefix, xrd_type, filesaver)
self.xrdcam = PerkinElmer_AD(prefix, filesaver=filesaver)
# self.xrdcam = Dexela_AD(prefix, filesaver=filesaver)
self.positioners = {}
for pname in conf.get('slow_positioners'):
self.positioners[pname] = self.PV(pname)
self.mapper.add_callback('Start', self.onStart)
self.mapper.add_callback('Abort', self.onAbort)
self.mapper.add_callback('basedir', self.onDirectoryChange)
self.prepare_beam_ok()
def __init__(self, mono_pv='13IDA:m65',
energy_pv='13IDE:En:', use_undulator=True):
self.xps = XPS()
self.mono = epics.Motor(mono_pv)
self.use_undulator = use_undulator
self.dspace_pv = epics.PV("%sdspace" % energy_pv)
self.traj = ''
self.backup_angle = 0 # angle scanned in ramp-up portion of trajectory
self.connect_xps()
self.nsegments = 3
self.struck = Struck('13IDE:SIS1:', scaler='13IDE:scaler1')
for i in range(8):
s = self.struck.get('mca%i' % (i+1))
class QXAFS_XPS:
host = '164.54.160.41'
port = 5001
timeout = 1
username = '******'
password = '******'
traj_folder = 'Public/Trajectories'
traj_name = 'qxafs.trj'
group_name = 'MONO'
positioners = 'THETA HEIGHT'
gather_outputs = ['MONO.THETA.SetpointPosition',
'MONO.THETA.CurrentPosition',
'MONO.THETA.FollowingError',
'MONO.THETA.SetpointVelocity',
'MONO.THETA.CurrentVelocity',
'MONO.THETA.SetpointAcceleration',
'MONO.THETA.CurrentAcceleration',
'MONO.HEIGHT.CurrentPosition',
]
def __init__(self, mono_pv='13IDA:m65',
energy_pv='13IDE:En:', use_undulator=True):
self.xps = XPS()
self.mono = epics.Motor(mono_pv)
self.use_undulator = use_undulator
self.dspace_pv = epics.PV("%sdspace" % energy_pv)
self.traj = ''
self.backup_angle = 0 # angle scanned in ramp-up portion of trajectory
self.connect_xps()
self.nsegments = 3
self.struck = Struck('13IDE:SIS1:', scaler='13IDE:scaler1')
for i in range(8):
s = self.struck.get('mca%i' % (i+1))
def connect_xps(self):
self.sid = self.xps.TCP_ConnectToServer(self.host, self.port, self.timeout)
self.xps.Login(self.sid, self.username, self.password)
time.sleep(0.25)
self.xps.GroupMotionEnable(self.sid, self.group_name)
def create_trajectory(self, dwelltime=10, span=1.00):
"""create a PVT trajectory file for a single linear motion
of length 'span' and time 'dt', with an offset ramp distance of 'ramp'
"""
dwelltime = abs(dwelltime)
sign = span / abs(span)
line_speed = span / dwelltime
max_accel = 50.0
ramp = span / 10.0
ramp_time = 1.5 * ramp/line_speed
ramp_accel = line_speed/ramp_time
count = 1
self.traj = ''
while abs(ramp_accel) > abs(max_accel):
ramp_time = ramp_time * 1.5
ramp = ramp * 1.5
ramp_accel = line_speed/ramp_time
count += 1
if count > 20:
print 'Could not compute a valid trajectory!'
return
yd_ramp = yd_line = yvelo = 0.00
xd_ramp, xd_line, xvelo = ramp, span, line_speed
# ramp_time = ramp_time*1.5
traj = [
"%f, %f, %f, %f, %f" % (ramp_time, xd_ramp, xvelo, yd_ramp, 0),
"%f, %f, %f, %f, %f" % (dwelltime, xd_line, xvelo, yd_line, yvelo),
"%f, %f, %f, %f, %f" % (ramp_time, xd_ramp, 0, yd_ramp, 0),
]
self.traj = traj
self.backup_angle = xd_ramp
def create_sinewave_traj(self, dtime=5.0, npts=100, n=5, yrange=1):
"""create sine wave trajectory:
arguments
----------
dtime time (sec) for total run
n number of periods
npts total number of pulses
yrange amplitude of oscillation
"""
self.dwelltime = dtime
i = np.arange(npts+1)
amp = yrange / 2.00
dt = dtime * 1.0/ npts
print dtime, npts, n
velo = amp * np.sin(i*2*np.pi*n/npts)
dist = dt * velo
self.traj = []
#o = open('sinex.dat', 'w')
#o.write('#\n#----------\n# t d v\n')
for d, v in zip(dist, velo):
self.traj.append("%.6f, %.6f, %.6f, 0, 0" % (dt, d, v))
#o.write("%.6f %.6f %.6f\n" % (dt, d, v))
#o.close()
self.backup_angle=0
def read_trajectory_file(self, fname):
f = open(fname, 'r')
self.traj = f.readlines()
dtime = 0
self.backup_angle = 0
for line in self.traj:
vals = [float(w) for w in line.split(',')]
if self.backup_angle == 0:
self.backup_angle = vals[1]
dtime = dtime + vals[0]
self.dwelltime = dtime
print 'Read Trajectory ', len(self.traj), self.dwelltime, self.backup_angle
self.start_angle = self.start_angle - self.backup_angle
print 'start angle = ', self.start_angle
def upload_trajectory(self):
text = StringIO('\n'.join(self.traj))
self.nsegments = len(self.traj)
ftpconn = ftplib.FTP()
ftpconn.connect(self.host)
ftpconn.login(self.username, self.password)
ftpconn.cwd(self.traj_folder)
ftpconn.storbinary('STOR %s' % self.traj_name, text)
ftpconn.close()
print 'uploaded trajectories'
def check_return(self, cmd, ret):
if ret[0] != 0:
print 'Command: ' , cmd, ' returned -> ', ret
raise ValueError
def read_gathering(self):
"read XPS gathering"
self.xps.GatheringStop(self.sid)
ret, npulses, nx = self.xps.GatheringCurrentNumberGet(self.sid)
print 'Read XPS Gathering ', ret, npulses, nx
counter = 0
while npulses < 1 and counter < 5:
counter += 1
time.sleep(1.0)
ret, npulses, nx = self.xps.GatheringCurrentNumberGet(self.sid)
print 'Had to do repeat XPS Gathering: ', ret, npulses, nx
ret, buff = self.xps.GatheringDataMultipleLinesGet(self.sid, 0, npulses)
if ret < 0: # gathering too long: need to read in chunks
print 'Need to read Data in Chunks!!!' # how many chunks are needed??
Nchunks = 3
nx = int( (npulses-2) / Nchunks)
ret = 1
while True:
time.sleep(0.1)
ret, xbuff = self.xps.GatheringDataMultipleLinesGet(self.sid, 0, nx)
if ret == 0:
break
Nchunks = Nchunks + 2
nx = int( (npulses-2) / Nchunks)
if Nchunks > 10:
print 'looks like something is wrong with the XPS!'
break
buff = [xbuff]
for i in range(1, Nchunks):
ret, xbuff = self.xps.GatheringDataMultipleLinesGet(self.sid, i*nx, nx)
buff.append(xbuff)
ret, xbuff = self.xps.GatheringDataMultipleLinesGet(self.sid, Nchunks*nx,
npulses-Nchunks*nx)
buff.append(xbuff)
buff = ''.join(buff)
print 'READ Gathering ', len(buff)
self.gather = buff[:]
for x in ';\r\t':
self.gather = self.gather.replace(x,' ')
def save_gathering(self, fname='qxafs_xps'):
gname = "%s_xps.000" % fname
sname = "%s_struck.000" % fname
gname = increment_filename(gname)
sname = increment_filename(sname)
f = open(gname, 'w')
f.write("# QXAFS Data saved %s\n" % time.ctime())
f.write("#-------------------\n")
f.write("# %s\n" % ' '.join(self.gather_outputs))
f.write(self.gather)
f.close()
time.sleep(0.1)
self.struck.saveMCAdata(fname = sname)
print 'Saved data: ', gname, ' / ', sname
return gname
def build_scan(self, energy1, energy2, dtime=2.0, npulses=1001):
dspace = self.dspace_pv.get()
a1 = en2angle(energy1, dspace)
a2 = en2angle(energy2, dspace)
da = int(100*(a1- a2))/100.0
self.energy1 = energy1
self.energy2 = energy2
self.start_angle = a1
self.npulses = npulses + 1
self.dwelltime = dtime
self.create_trajectory(dwelltime=dtime, span=(a2-a1))
self.upload_trajectory()
self.start_angle = a1 - self.backup_angle
print 'Built Scan OK'
def onStruckPulse(self, pvname=None, value=0, **kws):
if value % 25 == 0:
self.new_id_en = value
# print 'STruck value ', value
def prepare_scan(self, npulses=None):
""" put xps in Ready for Scan mode"""
self.clear_xps_events()
if npulses is not None:
self.npulses = npulses
if self.use_undulator:
self.set_undulator_scan()
dt = self.dwelltime / (self.npulses-1)
ret = self.xps.GatheringReset(self.sid)
ret = self.xps.MultipleAxesPVTPulseOutputSet(self.sid,
self.group_name, 1, self.nsegments, dt)
self.check_return('MultipleAxesPVTPulseOutputSet', ret)
ret = self.xps.MultipleAxesPVTPulseOutputGet(self.sid, self.group_name)
self.check_return('MultipleAxesPVTPulseOutputGet', ret)
ret = self.xps.MultipleAxesPVTVerification(self.sid,
self.group_name, self.traj_name)
self.check_return('MultipleAxesPVTVerification', ret)
ret = self.xps.GatheringConfigurationSet(self.sid, self.gather_outputs)
self.check_return('GatheringConfigurationSet', ret)
ret = self.xps.GatheringConfigurationGet(self.sid)
self.check_return('GatheringConfigurationGet', ret)
triggers = ('Always', 'MONO.PVT.TrajectoryPulse',)
ret = self.xps.EventExtendedConfigurationTriggerSet(self.sid, triggers,
('0','0'), ('0','0'),('0','0'),('0','0'))
self.check_return('EventExtConfTriggerSet', ret)
ret = self.xps.EventExtendedConfigurationActionSet(self.sid,
('GatheringOneData',), ('0',), ('0',),('0',),('0',))
self.check_return('EventExtConfActionSet', ret)
time.sleep(0.1)
print 'Scan Prepare OK'
def set_undulator_scan(self):
self.id_dat = np.loadtxt('Harmonic1.dat').transpose()
en = self.id_dat[0]
gap = self.id_dat[1]
gap1 = np.interp(self.energy1, en, gap)
gap2 = np.interp(self.energy2, en, gap)
epics.caput('ID13us:SSStartGap', gap1)
epics.caput('ID13us:SSEndGap', gap2)
epics.caput('ID13us:SSTime', self.dwelltime)
def execute_trajectory(self):
return self.xps.MultipleAxesPVTExecution(self.sid, self.group_name,
self.traj_name, 1)
def clear_xps_events(self):
"""clear any existing events"""
ret = self.xps.EventExtendedAllGet(self.sid)
if ret[0] == -83: # No Events Defined!
return
self.check_return('EventExtendedAllGet', ret)
for eventID in ret[1].split(';'):
ret = self.xps.EventExtendedRemove(self.sid, eventID)
self.check_return('EventExtRemove', ret)
def run(self):
"""run traj"""
print 'Run Trajectory'
if self.use_undulator:
id_offset = epics.caget('13IDE:En:id_off')
id1 = self.energy1/1000.0 + id_offset
id2 = self.energy2/1000.0 + id_offset
self.mono.move(self.start_angle)
if self.use_undulator:
epics.caput('13IDE:En:id_track', 0)
epics.caput('ID13us:ScanEnergy', id1)
struck_pv = epics.PV('13IDE:SIS1:CurrentChannel')
struck_pv.add_callback(self.onStruckPulse)
self.mono.move(self.start_angle, wait=True)
if self.use_undulator:
epics.caput('ID13us:SyncScanMode', 1)
print 'Before Trajectory: '
print ' Angle = ', epics.caget('13IDA:m65.VAL'), epics.caget('13IDA:m65.DVAL')
print ' Energy = ', epics.caget('13IDE:En:Energy')
print ' Und = ', epics.caget('ID13us:Energy')
self.struck.scaler.OneShotMode()
self.struck.ExternalMode()
self.struck.PresetReal = 0.0
time.sleep(0.010)
eventID, m = self.xps.EventExtendedStart(self.sid)
print 'Event : ', eventID, m
scan_thread = Thread(target=self.execute_trajectory)
if self.use_undulator:
epics.caput('ID13us:SSStart', 1)
print 'Waiting for Undulator Sync'
while True:
if epics.caget('ID13us:SSState') == 2:
break
self.struck.start()
scan_thread.start()
print 'ID scanning, started trajectory'
scan_thread.join()
print 'Trajectory Thread Done!'
ret = self.xps.GatheringStop(self.sid)
self.check_return('GatheringStop', ret)
self.struck.stop()
if self.use_undulator:
epics.caput('ID13us:SyncScanMode', 0)
class TrajectoryScan(object):
def __init__(self, xrf_prefix='13SDD1:', configfile=None):
self._pvs = {}
self.state = 'idle'
self.xmap = None
self.xsp3 = None
self.xrdcam = None
conf = self.mapconf = FastMapConfig(configfile)
print(" Using Configfile : ", configfile)
struck = conf.get('general', 'struck')
scaler = conf.get('general', 'scaler')
basedir = conf.get('general', 'basedir')
mapdb = conf.get('general', 'mapdb')
self.use_xrd = conf.get('xrd_ad', 'use')
self.use_xrf = conf.get('xrf', 'use')
self.xrf_type = conf.get('xrf', 'type')
self.xrf_pref = conf.get('xrf', 'prefix')
self.mapper = mapper(prefix=mapdb)
self.scan_t0 = time.time()
self.Connect_ENV_PVs()
self.ROI_Written = False
self.ENV_Written = False
self.ROWS_Written = False
self.xps = XPSTrajectory(**conf.get('xps'))
self.dtime = debugtime()
self.struck = Struck(struck, scaler=scaler)
self.struck.read_all_mcas()
print 'Using xrf type/prefix= ', self.xrf_type, self.xrf_pref
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap = MultiXMAP(self.xrf_pref)
elif self.xrf_type.startswith('xsp'):
self.xsp3 = Xspress3(self.xrf_pref, fileroot='/T/')
if self.use_xrd:
filesaver = conf.get('xrd_ad', 'fileplugin')
prefix = conf.get('xrd_ad', 'prefix')
xrd_type = conf.get('xrd_ad', 'type')
print(" Use XRD ", prefix, xrd_type, filesaver)
self.xrdcam = PerkinElmer_AD(prefix, filesaver=filesaver)
# self.xrdcam = Dexela_AD(prefix, filesaver=filesaver)
self.positioners = {}
for pname in conf.get('slow_positioners'):
self.positioners[pname] = self.PV(pname)
self.mapper.add_callback('Start', self.onStart)
self.mapper.add_callback('Abort', self.onAbort)
self.mapper.add_callback('basedir', self.onDirectoryChange)
self.prepare_beam_ok()
def prepare_beam_ok(self):
conf = self.mapconf.get('beam_ok')
self.flux_val_pv = self.PV(conf['flux_val_pv'])
self.flux_min_pv = self.PV(conf['flux_min_pv'])
self.shutter_status = [self.PV(x.strip()) for x in conf['shutter_status'].split('&')]
self.shutter_open = [self.PV(x.strip()) for x in conf['shutter_open'].split('&')]
def write(self, msg, flush=True):
sys.stdout.write("%s\n"% msg)
if flush:
sys.stdout.flush()
def PV(self, pvname):
"""return epics.PV for a device attribute"""
if pvname not in self._pvs:
self._pvs[pvname] = epics.PV(pvname)
if not self._pvs[pvname].connected:
self._pvs[pvname].wait_for_connection()
return self._pvs[pvname]
def onStart(self, pvname=None, value=None, **kw):
if value == 1:
self.state = 'start'
def onAbort(self, pvname=None, value=None, **kw):
if value == 1:
self.state = 'abort'
else:
self.state = 'idle'
def onDirectoryChange(self,value=None,char_value=None,**kw):
if char_value is not None:
os.chdir(os.path.abspath(nativepath(char_value)))
def setWorkingDirectory(self):
top_path = basepath(self.mapper.basedir)
basedir = os.path.abspath(nativepath(self.mapper.basedir))
try:
os.chdir(basedir)
except:
self.write('Cannot chdir to %s' % basedir)
fname = fix_filename(self.mapper.filename)
subdir = fname + '_rawmap'
counter = 0
while os.path.exists(subdir) and counter < 9999:
fname = increment_filename(fname)
subdir = fname + '_rawmap'
counter += 1
os.mkdir(subdir)
self.mapper.filename = fname
# write h5 file stub (with name of folder) for viewing program
h5fname = os.path.abspath(os.path.join(basedir, "%s.h5" % fname))
fout = open(h5fname, 'w')
fout.write("%s\n"% subdir)
fout.close()
self.mapper.workdir = subdir
self.workdir = os.path.abspath(os.path.join(basedir, subdir))
self.write('=Scan folder: %s' % self.workdir)
self.ROI_Written = False
self.ENV_Written = False
self.ROWS_Written = False
return subdir
def prescan(self, filename=None, filenumber=1, npulses=11,
scantime=1.0, **kw):
""" put all pieces (trajectory, struck, xmap) into
the proper modes for trajectory scan"""
self.npulses = npulses
self.mapper.setTime()
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap.setFileTemplate('%s%s.%4.4d')
self.xmap.setFileWriteMode(2)
self.xmap.MCAMode(filename='xmap', npulses=npulses)
self.xmap.setFileNumber(1)
elif self.xrf_type.startswith('xsp'):
self.xsp3.put('Acquire', 0)
self.xsp3.NumImages = min(16384, npulses + 1)
self.xsp3.setFileWriteMode(2)
self.xsp3.useExternalTrigger()
self.xsp3.setFileTemplate('%s%s.%4.4d')
self.xsp3.setFileName('xsp3')
self.xsp3.setFileNumber(1)
time.sleep(0.025)
self.xsp3.put('Acquire', 0, wait=True)
self.xsp3.put('ERASE', 1, wait=True)
if self.use_xrd:
self.xrdcam.setFilePath(winpath(self.workdir))
parent, subfolder = os.path.split(self.workdir)
# xrdpath = os.path.join("C:\\Data\\xas_user\\", subfolder)
# xrdpath = "C:\\Data\\xas_user\\"
# self.xrdcam.setFilePath(winpath(xrdpath))
time_per_pixel = scantime/(npulses-1)
# print 'PreScan XRD Camera: Time per pixel ', npulses, time_per_pixel
self.xrdcam.SetExposureTime(time_per_pixel)
self.xrdcam.SetMultiFrames(npulses)
self.xrdcam.setFileName('xrd')
time.sleep(0.25)
self.dtime.add('prescan xrf det')
self.struck.ExternalMode()
maxchan = self.struck.get('MaxChannels')
nstruck = min(maxchan, max(100, npulses+50))
self.struck.put('NuseAll', nstruck)
self.struck.put('Prescale', 1.0)
self.struck.put('PresetReal', 0.0)
self.dtime.add('prescan struck')
self.ROI_Written = False
self.ENV_Written = False
def postscan(self):
""" put all pieces (trajectory, struck, xmap) into
the non-trajectory scan mode"""
self.mapper.setTime()
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.Wait_XMAPWrite(irow=0)
self.dtime.add('postscan xmap data written')
self.xmap.SpectraMode()
self.dtime.add('postscan xmap in Spectra Mode')
else:
if self.xrf_type.startswith('xsp'):
self.Wait_Xspress3Write(irow=0)
time.sleep(0.25)
if self.use_xrd:
self.xrdcam.filePut('EnableCallbacks', 0)
self.xrdcam.ImageMode = 2
self.xrdcam.TriggerMode = 0
self.setIdle()
self.dtime.add('postscan done')
def save_positions(self, poslist=None):
plist = self.positioners.keys()
if poslist is not None:
for p in poslist:
if p not in plist:
plist.append(p)
self.__savedpos={}
for pvname in plist:
self.__savedpos[pvname] = self.PV(pvname).get()
self.dtime.add('save_positions done')
def restore_positions(self):
for pvname,val in self.__savedpos.items():
self.PV(pvname).put(val)
self.dtime.add('restore_positions done')
def Wait_XMAPWrite(self, irow=0):
"""wait for XMAP to finish writing its data"""
fnum = irow
# print 'Wait for XRF file', self.use_xrf, self.xrf_type
if self.use_xrf and self.xrf_type.startswith('xmap'):
# wait for previous netcdf file to be written
t0 = time.time()
time.sleep(0.1)
if not self.xmap.FileWriteComplete():
xmap_ok, npix = self.xmap.finish_pixels(timeout=5.0)
self.rowdata_ok = xmap_ok
if not xmap_ok:
self.write('Bad data -- XMAP too few pixels')
while not self.xmap.FileWriteComplete():
time.sleep(0.25)
if time.time()-t0 > 3.0:
self.mapper.message = 'XMAP File Writing Not Complete!'
self.rowdata_ok = False
self.xmap.FileCaptureOff()
time.sleep(0.5)
self.xmap.SpectraMode()
time.sleep(0.5)
self.xmap.MCAMode(filename='xmap', npulses=self.npulses)
time.sleep(0.5)
print 'XMAP could not complete file writing!'
self.write('Bad data -- XMAP could not complete file writing')
break
xmap_fname = nativepath(self.xmap.getLastFileName())[:-1]
folder,xmap_fname = os.path.split(xmap_fname)
prefix, suffix = os.path.splitext(xmap_fname)
suffix = suffix.replace('.','')
try:
fnum = int(suffix)
except:
fnum = 1
return fnum
def Wait_Xspress3Write(self, irow=0):
"""wait for Xspress3 to finish writing its data"""
fnum = irow
if self.use_xrf and self.xrf_type.startswith('xsp'):
# wait for previous file writing to complete
if not self.xsp3.FileWriteComplete():
t0 = time.time()
while not self.xsp3.FileWriteComplete() and (time.time()-t0 < 5.0):
time.sleep(0.1)
if not self.xsp3.FileWriteComplete():
self.mapper.message = 'Xspress3 File Writing Not Complete!'
self.rowdata_ok = False
time.sleep(0.5)
self.xsp3.stop()
time.sleep(0.5)
self.write('Bad data -- Xspress3 could not complete file writing')
x_fname = nativepath(self.xsp3.getLastFileName())[:-1]
folder, x_fname = os.path.split(x_fname)
prefix, suffix = os.path.splitext(x_fname)
suffix = suffix.replace('.','')
try:
fnum = int(suffix)
except:
fnum = 1
return fnum
def run_scan(self, filename='TestMap',scantime=10, accel=None,
pos1='13XRM:m1', start1=0, stop1=1, step1=0.1,
dimension=1,
pos2=None, start2=0, stop2=1, step2=0.1, **kws):
self.dtime.clear()
if pos1 not in self.positioners:
raise ValueError(' %s is not a trajectory positioner' % pos1)
self.mapper.status = 1
npts1, start1, stop1, step1 = fix_range(start1, stop1, step1, addstep=True)
step2_positive = start2 < stop2
npts2, start2, stop2, step2 = fix_range(start2, stop2, step2, addstep=False)
if not step2_positive:
start2, stop2 = stop2, start2
step2 = -step2
# set offset for whether to start with foreward or backward trajectory
dir_offset = 0
if start1 > stop1:
dir_offset = 1
self.mapper.npts = npts1
self.mapper.setNrow(0)
self.mapper.maxrow = npts2
self.mapper.info = 'Pending'
self.mapper.message = "will execute %i points in %.2f sec" % (npts1,scantime)
self.state = 'pending'
self.save_positions()
self.dtime.add( 'Saved Positions')
if pos2 is None:
dimension = 1
npts2 = 1
self.nrows_expected = npts2
self.scan_t0 = time.time()
self.MasterFile.write('#SCAN.version = %s\n' % SCAN_VERSION)
self.MasterFile.write('#SCAN.starttime = %s\n' % time.ctime())
self.MasterFile.write('#SCAN.filename = %s\n' % filename)
self.MasterFile.write('#SCAN.dimension = %i\n' % dimension)
self.MasterFile.write('#SCAN.nrows_expected = %i\n' % npts2)
self.MasterFile.write('#SCAN.time_per_row_expected = %.2f\n' % scantime)
self.MasterFile.write('#Y.positioner = %s\n' % str(pos2))
self.MasterFile.write('#Y.start_stop_step = %f, %f, %f \n' % (start2, stop2, step2))
self.MasterFile.write('#------------------------------------\n')
self.MasterFile.write('# yposition xmap_file struck_file xps_file time\n')
self.dtime.add( 'Master header')
kw = dict(scantime=scantime, accel=accel,
filename=self.mapper.filename, filenumber=0,
dimension=dimension, npulses=npts1-1, scan_pt=1)
axis1 = self.mapconf.get('fast_positioners', pos1).upper()
linescan = dict(start=start1, stop=stop1, step=step1,
axis=axis1, scantime=scantime, accel=accel)
if not self.xps.DefineLineTrajectories(**linescan):
print 'Failed to define trajectory!!'
self.postscan()
return
print 'Run_Scan: Defined Trajectories'
self.dtime.add('trajectory defined')
# move to starting position
dir_offset += POSITIONER_OFFSETS[axis1]
p1_start = start1
if dir_offset % 2 != 0:
p1_start = stop1
self.PV(pos1).put(p1_start, wait=False)
self.dtime.add( 'put #1 done')
if dimension > 1:
self.PV(pos2).put(start2, wait=False)
self.dtime.add('put positioners to starting positions')
self.prescan(**kw)
self.dtime.add( 'prescan done')
self.PV(pos1).put(p1_start, wait=True)
if dimension > 1:
self.PV(pos2).put(start2, wait=True)
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap.FileCaptureOn()
elif self.xrf_type.startswith('xsp'):
pass
irow = 0
while irow < npts2:
self.mapper.status = 1
self.rowdata_ok = True
irow = irow + 1
self.dtime.add('======== map row %i ' % irow)
# print 'ROW ', irow, start1, stop1, step1, dir_offset
dirx = (dir_offset + irow) % 2
traj, p1_this, p1_next = [('backward', stop1, start1),
('foreward', start1, stop1)][dirx]
if dimension > 1:
self.mapper.info = 'Row %i / %i (%s)' % (irow,npts2,traj)
else:
self.mapper.info = 'Scanning'
self.mapper.setTime()
kw['filenumber'] = irow
kw['scan_pt'] = irow
if self.state == 'abort':
self.mapper.message = 'Map aborted before starting!'
break
ypos = 0
self.PV(pos1).put(p1_this, wait=True)
if dimension > 1:
self.PV(pos2).put(start2 + (irow-1)*step2, wait=True)
self.dtime.add('positioners ready %.5f' % p1_this)
if dimension > 1:
ypos = self.PV(pos2).get()
self.mapper.status = 2
self.dtime.add('before exec traj')
mt0 = time.time()
self.ExecuteTrajectory(name=traj, **kw)
self.mapper.status = 3
self.dtime.add('after exec traj')
if dimension > 1:
self.PV(pos2).put(start2 + irow*step2, wait=False)
self.PV(pos1).put(p1_next, wait=False)
# note:
# First WriteRowData will write data from XPS and struck,
# Then we wait for the XMAP to finish writing its data.
nxps, nxmap, rowinfo = self.WriteRowData(scan_pt=irow,
ypos=ypos,
npts=npts1)
if irow % 5 == 0:
self.write('row %i/%i' % (irow, npts2))
self.dtime.add('xrf data saved')
if not self.rowdata_ok:
self.write('Bad data for row: redoing this row')
irow = irow - 1
self.PV(pos1).put(p1_this, wait=False)
else:
self.MasterFile.write(rowinfo)
self.MasterFile.flush()
self.mapper.setTime()
self.mapper.setNrow(irow)
if self.state == 'abort':
self.mapper.message = 'Map aborted!'
break
self.check_beam_ok()
self.dtime.add('row done')
# self.dtime.show(clear=True)
# print 'Restore positions..'
self.restore_positions()
self.mapper.info = "Finished"
self.dtime.add('after writing last row')
self.postscan()
self.write('done.')
self.dtime.add('map after postscan')
# self.dtime.show()
self.dtime.clear()
def check_beam_ok(self, timeout=120):
conf = self.mapconf.get('beam_ok')
flux_min = float(self.flux_min_pv.get())
flux_val = float(self.flux_val_pv.get())
if flux_val > flux_min:
return
if flux_min < 400.0:
print(" BEAM OK BY Cheating low Flux Level")
return
# if we get here, we'll want to redo the previous row
self.rowdata_ok = False
print 'Flux low... checking shutters'
def shutters_open():
return all([x.get()==1 for x in self.shutter_status])
shutter_ok = shutters_open()
t0 = time.time()
while not shutter_ok:
for sh_open in self.shutter_open:
sh_open.put(1)
time.sleep(0.50)
shutter_ok = shutters_open()
if self.state == 'abort' or time.time() > t0 + timeout:
return
# shutters are open.... check flux again,
# adjust mono if needed.
time.sleep(2.0)
flux_min = float(self.flux_min_pv.get())
flux_val = float(self.flux_val_pv.get())
if flux_val < flux_min and USE_MONO_CONTROL:
set_mono_tilt()
return
def ExecuteTrajectory(self, name='line', filename='TestMap',
scan_pt=1, scantime=10, dimension=1,
npulses=11, wait=False, **kw):
""" run individual trajectory"""
t0 = time.time()
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap.setFileNumber(scan_pt)
self.xmap.FileCaptureOn()
time.sleep(0.1)
self.xmap.EraseStart = 1
while self.xmap.Acquiring != 1 and time.time()-t0 < 10.0:
self.xmap.EraseStart = 1
time.sleep(0.1)
self.dtime.add('exec: xmap armed? %s' % (repr(1==self.xmap.Acquiring)))
elif self.xrf_type.startswith('xsp'):
# complex Acquire On / FileCapture On:
self.xsp3.setFileNumber(scan_pt)
self.xsp3.put('Acquire', 0, wait=True)
self.xsp3.put('ERASE', 1, wait=True)
self.xsp3.FileCaptureOn()
time.sleep(0.1)
self.xsp3.Acquire = 1
time.sleep(0.05)
if self.use_xrd:
self.xrdcam.setFileNumber(scan_pt)
self.xrdcam.StartStreaming()
self.struck.start()
time.sleep(0.05)
self.mapper.PV('Abort').put(0)
self.dtime.add('exec: struck started.')
self.mapper.setTime()
# self.write('Ready to start trajectory')
scan_thread = Thread(target=self.xps.RunLineTrajectory,
kwargs=dict(name=name, save=False),
name='scannerthread')
scan_thread.start()
self.state = 'scanning'
self.dtime.add('ExecTraj: traj thread begun')
t0 = time.time()
if self.use_xrf and not self.ROI_Written:
xrfdet = self.xmap
if self.xrf_type.startswith('xsp'):
xrfdet = self.xsp3
fout = os.path.join(self.workdir, 'ROI.dat')
# print(" SAVE ROI.dat to ", fout, xrfdet)
if True: # try:
fh = open(fout, 'w')
fh.write('\n'.join(xrfdet.roi_calib_info()))
fh.close()
self.ROI_Written = True
self.dtime.add('ExecTraj: ROI done')
else:# except:
self.dtime.add('ExecTraj: ROI saving failed!!')
if not self.ENV_Written:
fout = os.path.join(self.workdir, 'Environ.dat')
self.Write_EnvData(filename=fout)
self.ENV_Written = True
self.dtime.add('ExecTraj: Env done')
# now wait for scanning thread to complete
scan_thread.join()
beacon_time = time.time()
while scan_thread.isAlive() and time.time()-t0 < scantime+5.0:
epics.poll()
time.sleep(0.002)
if time.time() - beacon_time > 5.0:
self.mapper.setTime()
beacon_time = time.time()
# wait for Xspress3 to finish
if self.use_xrf and self.xrf_type.startswith('xsp'):
if self.xsp3.DetectorState_RBV not in (0, 10):
xsp3_ready = False
count = 0
while not xsp3_ready:
xsp3_ready = self.xsp3.DetectorState_RBV in (0, 10)
xsp3_ready = xsp3_ready or (count > 50)
time.sleep(0.1)
count = count + 1
if count > 10:
self.xsp3.Acquire = 0
self.xsp3.FileCaptureOff()
self.dtime.add('ExecTraj: Scan Thread complete.')
time.sleep(0.05)
def WriteEscanData(self):
self.escan_saver.folder = self.workdir
try:
new_lines = self.escan_saver.process()
except:
new_lines = 0
if new_lines < 0:
return
self.data_fname = os.path.abspath(os.path.join(nativepath(self.mapper.basedir),
self.mapper.filename))
if os.path.isdir(self.data_fname) or '.' not in self.data_fname:
self.mapper.filename = increment_filename("%s.000" % self.mapper.filename)
self.data_fname = os.path.abspath(os.path.join(nativepath(self.mapper.basedir),
self.mapper.filename))
if new_lines > 0:
try:
f = open(self.data_fname, self.data_mode)
f.write("%s\n" % '\n'.join(self.escan_saver.buff))
f.close()
except IOError:
self.write('WARNING: Could not write Scan Data to ESCAN Format')
self.data_mode = 'a'
try:
self.escan_saver.clear()
except:
pass
def WriteRowData(self, filename='TestMap', scan_pt=1, ypos=0, npts=None):
# NOTE:!! should return here, write files separately.
self.struck.stop()
strk_fname = self.make_filename('struck', scan_pt)
xps_fname = self.make_filename('xps', scan_pt)
if self.use_xrf and self.xrf_type.startswith('xmap'):
xrf_fname = self.make_filename('xmap', scan_pt)
elif self.use_xrf and self.xrf_type.startswith('xsp'):
xrf_fname = self.make_filename('xsp3', scan_pt)
self.dtime.add('Write Row Data: start %i, ypos=%f ' % (scan_pt, ypos))
saver_thread = Thread(target=self.xps.SaveResults, name='saver',
args=(xps_fname,))
saver_thread.start()
# self.xps.SaveResults(xps_fname)
nxmap = 0
self.dtime.add('Write: start xps save thread')
if self.use_xrf and self.xrf_type.startswith('xmap'):
xrf_fname = nativepath(self.xmap.getFileNameByIndex(scan_pt))[:-1]
nxmap = self.Wait_XMAPWrite(irow=scan_pt)
elif self.use_xrf and self.xrf_type.startswith('xsp'):
nxmap = self.Wait_Xspress3Write(irow=scan_pt)
self.dtime.add('Write: xrf data saved')
wrote_struck = False
t0 = time.time()
counter = 0
n_sis = -1
while not wrote_struck and time.time()-t0 < 15.0:
counter = counter + 1
try:
nsmcas, nspts = self.struck.saveMCAdata(fname=strk_fname)
n_sis = nspts
wrote_struck = (self.struck.CurrentChannel - nspts) < 2
except:
print 'trouble saving struck data.. will retry'
time.sleep(0.05 + 0.2*counter)
if not wrote_struck:
self.rowdata_ok = False
self.write('Bad data -- Could not SAVE STRUCK DATA!')
self.dtime.add('Write: struck saved (%i tries)' % counter)
saver_thread.join()
self.dtime.add('Write: xps saved')
rowinfo = self.make_rowinfo(xrf_fname, strk_fname, xps_fname, ypos=ypos)
if self.use_xrd:
if not self.xrdcam.FinishStreaming(timeout=15.0):
self.write('Bad data: not enough XRD captures: %i' %
self.xrdcam.fileGet('NumCaptured_RBV'))
self.xrdcam.ResetStreaming()
self.rowdata_ok = False
n_xps = self.xps.nlines_out
n_xrf = -1
if self.use_xrf and self.xrf_type.startswith('xmap'):
n_xrf = self.xmap.PixelsPerRun
elif self.use_xrf and self.xrf_type.startswith('xsp'):
n_xrf = self.xsp3.NumImages_RBV
sys.stdout.write(ROW_MSG % (scan_pt, n_xps, n_sis, n_xrf))
sys.stdout.flush()
self.dtime.add('WriteRowData done: %i, %s' %(self.xps.nlines_out, rowinfo))
return (self.xps.nlines_out, nxmap, rowinfo)
def make_filename(self, name, number):
fout = os.path.join(self.workdir, "%s.%4.4i" % (name,number))
return os.path.abspath(fout)
def make_rowinfo(self, x_fname, s_fname, g_fname, ypos=0):
x = os.path.split(x_fname)[1]
s = os.path.split(s_fname)[1]
g = os.path.split(g_fname)[1]
dt = time.time() - self.scan_t0
return '%.4f %s %s %s %9.2f\n' % (ypos, x, s, g, dt)
def Write_EnvData(self,filename='Environ.dat'):
fh = open(filename,'w')
for pvname, title, pv in self.env_pvs:
val = pv.get(as_string=True)
fh.write("; %s (%s) = %s \n" % (title,pvname,val))
fh.close()
def Connect_ENV_PVs(self):
self.env_pvs = []
envfile = self.mapconf.get('general', 'envfile')
try:
f = open(envfile,'r')
lines = f.readlines()
f.close()
except:
self.write('ENV_FILE: could not read %s' % envfile)
return
for line in lines:
words = line.split(' ', 1)
pvname =words[0].strip().rstrip()
if len(pvname) < 2 or pvname.startswith('#'): continue
title = pvname
try:
title = words[1][:-1].strip().rstrip()
except:
pass
if pvname not in self.env_pvs:
self.env_pvs.append((pvname, title, epics.PV(pvname)))
return
def setIdle(self):
self.state = self.mapper.info = 'idle'
self.mapper.ClearAbort()
self.mapper.status = 0
self.mapper.setTime()
def StartScan(self):
self.dtime.clear()
self.dtime.add(' set working folder')
subdir = self.setWorkingDirectory()
top_path = basepath(self.mapper.basedir)
self.mapconf.Read(os.path.abspath(self.mapper.scanfile) )
conf = self.mapconf
self.use_xrd = conf.get('xrd_ad', 'use')
det_path = os.path.join(top_path, subdir)
if self.use_xrd:
filesaver = conf.get('xrd_ad', 'fileplugin')
prefix = conf.get('xrd_ad', 'prefix')
xrd_type = conf.get('xrd_ad', 'type')
print(" Use XRD ", prefix, xrd_type, filesaver)
self.xrdcam = PerkinElmer_AD(prefix, filesaver=filesaver)
# self.xrdcam = Dexela_AD(prefix, filesaver=filesaver)
# self.xrdcam.setFilePath(winpath("C:\\Data\\xas_user\\"))
if self.use_xrf:
if self.xrf_type.startswith('xmap'):
self.xmap.setFilePath(winpath(det_path))
self.xmap.SpectraMode()
self.xmap.start()
elif self.xrf_type.startswith('xsp'):
self.xsp3.setFilePath(det_path)
self.check_beam_ok()
self.dtime.add(' read config')
self.mapper.message = 'preparing scan...'
self.mapper.info = 'Starting'
fname = fix_filename(self.mapper.filename)
self.mapconf.set_datafilename(fname)
self.dtime.add('set datafile')
self.MasterFile = open(os.path.join(self.workdir, 'Master.dat'), 'w')
self.mapconf.Save(os.path.join(self.workdir, 'Scan.ini'))
self.dtime.add(' saved scan.ini')
self.data_mode = 'w'
# self.escan_saver = EscanWriter(folder=self.workdir)
scan = self.mapconf.get('scan')
scan['scantime'] = scan['time1']
if scan['dimension'] == 1:
scan['pos2'] = None
scan['start2'] = 0
scan['stop2'] = 0
scan['filename'] = self.mapper.filename
# print 'Scan FileName is ', scan['filename']
# self.dtime.show()
self.run_scan(**scan)
self.MasterFile.close()
self.mapper.message = 'Scan finished: %s' % (scan['filename'])
self.setIdle()
# self.dtime.show()
def mainloop(self):
self.write('FastMap collector starting up... %s' % (time.ctime()))
self.mapper.ClearAbort()
self.mapper.setTime()
self.mapper.message = 'Ready to Start Map'
self.mapper.info = 'Ready'
self.setIdle()
epics.poll()
time.sleep(0.10)
t0 = time.time()
self.state = 'idle'
self.write('FastMap collector ready.')
while True:
try:
epics.poll()
if time.time()-t0 > 0.2:
t0 = time.time()
self.mapper.setTime()
if self.state == 'start':
self.mapper.AbortScan()
self.StartScan()
elif self.state == 'abort':
self.write('Fastmap aborting')
self.mapper.ClearAbort()
time.sleep(0.5)
self.state = 'idle'
elif self.state == 'pending':
self.write('Fastmap state=pending')
elif self.state == 'reboot':
self.mapper.info = 'Rebooting'
sys.exit()
elif self.state == 'waiting':
self.mapper.ClearAbort()
elif self.state != 'idle':
self.write('Fastmap: unknown state: %s' % self.state)
time.sleep(0.01)
except KeyboardInterrupt:
break
