def Run(self):
try:
self.Log = LogFile(self.Args.logfile)
except IOError:
print "File: " + self.Log.Filename + " cannot be opened : " + str(
sys.exc_info()[1])
#TODO: log to stderr
raise IOError()
#if args.v > 0 : print "Processing Log File " + log.Filename + ":" + str(log.Length) + " bytes"
logline = self.Log.RetrieveCurrentLine()
widgets = [
'Processing potential messages: ',
progressbar.Percentage(), ' ',
progressbar.Bar(marker=progressbar.RotatingMarker()), ' ',
progressbar.ETA()
]
if self.Args.quiet is False:
pbar = progressbar.ProgressBar(widgets=widgets, maxval=100).start()
while logline != "": #TODO: Make this actually exit on EOF
self.IsMatch(logline)
if self.Args.quiet is False:
pbar.update((1.0 * self.Log.Position / self.Log.Length) * 100)
logline = self.Log.RetrieveCurrentLine()
if self.Args.quiet is False: pbar.finish()
def log(self, msg): msg = 'PSA[%s@%s]: %s' % (self.Name, self.Root, msg) if LogFile: LogFile.log(msg) else: print msg sys.stdout.flush()
def connectToAddr():
con = paramiko.SSHClient()
con.set_missing_host_key_policy(paramiko.AutoAddPolicy())
#print(server_addr.get())
con.connect(server_addr.get(),username=config['auth']['username'],
password=config['auth']['password'])
name = server_addr.get()
name = name[:name.find('.')]
connections[name]=con
#print("name: ", name)
tree.insert('','end',server_addr.get(),text=name,value=con,tags=('clicky','simple'))
tree.tag_bind('clicky','<ButtonRelease-3>',itemClicked)
#sftp = con.open_sftp()
logs = []
for log in config['logs']:
logs.append(resolve_log(con,log))
for log in logs:
#print("log: ",log[0])
try:
logf = LogFile(frame,filterFrame,con,log[0],server_addr.get(),tempdir)
log_files[logf.getName()] = logf
parent = tree.insert(server_addr.get(),'end',server_addr.get()+log[0],text=logf.name,
values=logf.getName(),tags=('selected'))
tree.tag_bind('selected','<ButtonRelease-1>',logSelected)
except Exception as e:
print("woopies! something went wrong with main log: ",e)
continue
def __init__(self, request, filename=None, buffer_size=65536, **kw):
if filename == None:
rootpagename = kw.get('rootpagename', None)
if rootpagename:
from MoinMoin.Page import Page
filename = Page(request, rootpagename).getPagePath('event-log', isfile=1)
else:
filename = request.rootpage.getPagePath('event-log', isfile=1)
LogFile.__init__(self, filename, buffer_size)
class LoPhiLogger(multiprocessing.Process):
"""
This class will continuously read in data from a queue and write to
the specified log file(s).
"""
def __init__(self,
data_queue,
filename=G.DEFAULT_LOG_FILE,
filetype="tsv",
packed_data=False):
"""
Initialize our logger to read from a queue and write to files
"""
# Packed in protobuf or just a dict?
self.packed_data = packed_data
# Remember our input queue
self.DATA_QUEUE = data_queue
# Create our log file
self.logfile = LogFile(filename,
reprint_header=False,
output_type=filetype)
multiprocessing.Process.__init__(self)
def run(self):
"""
Loop forever consuming output from our SUA threads
"""
# Wait for output to start returning, and handle appropriately
while True:
# Get our log data
output_packed = self.DATA_QUEUE.get()
# If its a kill command, just post it
if output_packed == G.CTRL_CMD_KILL:
logger.debug("Logger killed...")
# Close our logs cleanly
for log in self.logfiles.keys():
self.logfiles[log].close()
break
if self.packed_data:
output = protobuf.unpack_sensor_output(output_packed)
else:
output = output_packed
# Log to file
self.logfile.append(output)
logger.debug("Logger closed.")
def __init__(self, request, filename=None, buffer_size=65536, **kw):
if filename == None:
rootpagename = kw.get('rootpagename', None)
if rootpagename:
filename = Page(request, rootpagename).getPagePath('edit-log', isfile=1)
else:
filename = request.rootpage.getPagePath('edit-log', isfile=1)
LogFile.__init__(self, filename, buffer_size)
self._NUM_FIELDS = 9
self._usercache = {}
# Used by antispam in order to show an internal name instead
# of a confusing userid
self.uid_override = kw.get('uid_override', None)
def _ping(self, host):
"""
Ping one host and set status to a Zipato sensor.
:param str host: Target host.
:rtype: str
:returns: Status message
"""
message_log = LogFile(self.MESSAGE_LOG)
if host in self.PING_HOSTS.keys():
ep = self.PING_HOSTS[host]['ep']
apikey = self.PING_HOSTS[host]['apikey']
else:
message = (
"ping: host={}, Host has not been configured for ping")
message = message.format(host)
message_log.write([message])
return None
try:
for i in range(self.PING_COUNT):
command = "{}ping -c {} {}"
command = command.format(
self.PING_PATH, str(self.PING_COUNT), host)
p = subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
shell=True)
stdout, stderr = p.communicate()
result = re.match('.*0 received.*', str(stdout), re.DOTALL)
status = result is None
if status:
break
sleep(self.PING_INTERVAL)
# Set the status of a Zipato sensor to the ping status
zipato_connection = ZipatoConnection(self.ZIPATO_SERIAL)
if status:
zipato_connection.set_sensor_status(
ep=ep, apikey=apikey, status=True)
else:
zipato_connection.set_sensor_status(
ep=ep, apikey=apikey, status=False)
except:
error_log = LogFile(self.ERROR_LOG)
message = 'ping: host={}'.format(host)
error_log.write([message])
traceback_message = traceback.format_exc()
error_log.write([traceback_message], date_time=False)
message = "ping: host={}, status={}".format(host, status)
message_log.write([message])
class LoPhiLogger(multiprocessing.Process):
"""
This class will continuously read in data from a queue and write to
the specified log file(s).
"""
def __init__(self, data_queue, filename=G.DEFAULT_LOG_FILE, filetype="tsv", packed_data=False):
"""
Initialize our logger to read from a queue and write to files
"""
# Packed in protobuf or just a dict?
self.packed_data = packed_data
# Remember our input queue
self.DATA_QUEUE = data_queue
# Create our log file
self.logfile = LogFile(filename, reprint_header=False, output_type=filetype)
multiprocessing.Process.__init__(self)
def run(self):
"""
Loop forever consuming output from our SUA threads
"""
# Wait for output to start returning, and handle appropriately
while True:
# Get our log data
output_packed = self.DATA_QUEUE.get()
# If its a kill command, just post it
if output_packed == G.CTRL_CMD_KILL:
logger.debug("Logger killed...")
# Close our logs cleanly
for log in self.logfiles.keys():
self.logfiles[log].close()
break
if self.packed_data:
output = protobuf.unpack_sensor_output(output_packed)
else:
output = output_packed
# Log to file
self.logfile.append(output)
logger.debug("Logger closed.")
def connectToAddr():
## con = paramiko.SSHClient()
## con.set_missing_host_key_policy(paramiko.AutoAddPolicy())
## #print(server_addr.get())
## con.connect(server_addr.get(),username=config['auth']['username'],
## password=config['auth']['password'])
name = server_addr.get()
name = name[:name.find('.')]
con = connection.Connection(server_addr.get(), config['auth']['username'],
config['auth']['password'], name)
connections[name] = con
#print("name: ", name)
tree.insert('',
'end',
server_addr.get(),
text=name,
value=('', con),
tags=('clicky', 'simple'))
tree.tag_bind('clicky', '<ButtonRelease-3>', itemClicked)
#sftp = con.open_sftp()
logs = []
for log in config['logs']:
logs.append(resolve_log(con, log))
for log in logs:
#print("log: ",log[0])
try:
logf = LogFile(frame, filterFrame, con, log[0], server_addr.get(),
tempdir)
if not logf.checkExists():
print("Log file doesn't exist: ", log[0])
continue
log_files[logf.getName()] = logf
parent = tree.insert(server_addr.get(),
'end',
server_addr.get() + log[0],
text=logf.name,
values=(logf.lastEdit, logf.getName()),
tags=('selected'))
#tree.set(parent,'updated',)
tree.tag_bind('selected', '<ButtonRelease-1>', logSelected)
except Exception as e:
print("woopies! something went wrong with main log: ", e)
continue
def __init__(self,
data_queue,
filename=G.DEFAULT_LOG_FILE,
filetype="tsv",
packed_data=False):
"""
Initialize our logger to read from a queue and write to files
"""
# Packed in protobuf or just a dict?
self.packed_data = packed_data
# Remember our input queue
self.DATA_QUEUE = data_queue
# Create our log file
self.logfile = LogFile(filename,
reprint_header=False,
output_type=filetype)
multiprocessing.Process.__init__(self)
def __init__(self, data_queue, filename=G.DEFAULT_LOG_FILE, filetype="tsv", packed_data=False):
"""
Initialize our logger to read from a queue and write to files
"""
# Packed in protobuf or just a dict?
self.packed_data = packed_data
# Remember our input queue
self.DATA_QUEUE = data_queue
# Create our log file
self.logfile = LogFile(filename, reprint_header=False, output_type=filetype)
multiprocessing.Process.__init__(self)
class TestLogFile(unittest.TestCase):
LOGPATH = "/tmp/log.html.gz"
JOBPATH = "/tmp"
JOB = "testjob"
def setUp(self):
self.logfile = LogFile(self.LOGPATH, self.JOBPATH, self.JOB)
def test_mkdir_log_path(self):
self.logfile.mkdir_job_path()
self.assertTrue(os.path.isdir(self.logfile.jobpath))
def test_unzip_log_file(self):
self.logfile.mkdir_job_path()
self.logfile.unzip_log_file()
fname = "{}/log.html".format(self.logfile.jobpath)
self.assertTrue(os.path.isfile(fname))
def test_parse_log(self):
self.logfile.parse_log(None)
Env.COLOR_BLUE = Env.color and "\033[1;34m" or ""
Env.COLOR_GREEN = Env.color and "\033[1;32m" or ""
Env.COLOR_YELLOW = Env.color and "\033[1;33m" or ""
Env.COLOR_RED = Env.color and "\033[1;31m" or ""
Env.COLOR_CYAN = Env.color and "\033[1;36m" or ""
Env.fcgi_cgi = which('fcgi-cgi')
Env.dir = mkdtemp(suffix='-l2-tests')
Env.defaultwww = os.path.join(Env.dir, "www", "default")
Env.log = open(os.path.join(Env.dir, "tests.log"), "w")
if Env.color: Env.log = RemoveEscapeSeq(Env.log)
if Env.debug:
logfile = Env.log
Env.log = LogFile(sys.stdout, **{"[log]": logfile})
sys.stderr = LogFile(sys.stderr, **{"[stderr]": logfile})
sys.stdout = LogFile(sys.stdout, **{"[stdout]": logfile})
else:
Env.log = LogFile(Env.log)
sys.stderr = LogFile(sys.stderr, **{"[stderr]": Env.log})
sys.stdout = LogFile(sys.stdout, **{"[stdout]": Env.log})
failed = False
try:
# run tests
tests = Tests()
tests.LoadTests()
failed = True
try:
class Xray_Beam_Stabilization(object):
name = "xray_beam_stabilization"
log = LogFile(name+".log",["date time","filename","x","y","x_control","y_control","image_timestamp"])
if log.filename == "":
log.filename = "//mx340hs/data/anfinrud_1702/Logfiles/xray_beam_stabilization.log"
auto_update = False
x_PV = persistent_property("x_PV","14IDC:mir2Th.VAL") # Piezo control voltage in V
x_read_PV = persistent_property("x_read_PV","14IDC:mir2Th.RBV")
y_PV = persistent_property("y_PV","14IDA:DAC1_4.VAL") # Theta in mrad
y_read_PV = persistent_property("y_read_PV","14IDA:DAC1_4.VAL")
x_gain = persistent_property("x_gain",0.143) # mrad/mm
y_gain = persistent_property("y_gain",2.7) # V/mm was: 1/3.3e-3
x_nominal = persistent_property("x_nominal",175.927) # mm from left, 2016-03-05
y_nominal = persistent_property("y_nominal",174.121) # mm from top, 2016-03-05
history_length = persistent_property("history_length",5)
average_samples = persistent_property("average_samples",5)
x_enabled = False
y_enabled = False
ROI_width = persistent_property("ROI_width",1.0) # mm
x_ROI_center = persistent_property("x_ROI_center",175.9) # mm from left
y_ROI_center = persistent_property("y_ROI_center",174.1) # mm from top
min_SNR = persistent_property("min_SNR",5.0) # signal-to-noise ratio
# Use only images matching this pattern, e.g. "5pulses"
history_filter = persistent_property("history_filter","")
analysis_filter = persistent_property("analysis_filter","")
def __init__(self):
""""""
start_new_thread(self.keep_updated,())
def keep_updated(self):
while True:
try:
if self.auto_update: self.update()
if self.x_enabled: self.apply_x_correction()
if self.y_enabled: self.apply_y_correction()
except Exception,m: info("xray_beam_stabilization: %s" % m); break
sleep(1)
def update(self):
t = self.image_timestamp
if t != 0 and abs(t - self.last_image_timestamp) >= 0.1:
f = self.image_basename
x,y = self.beam_position
xc,yc = self.x_control,self.y_control
self.log.log(f,x,y,xc,yc,t)
@property
def x_average(self): return average(self.x_samples)
@property
def y_average(self): return average(self.y_samples)
@property
def x_history(self): return self.history("x",count=self.history_length)
@property
def y_history(self): return self.history("y",count=self.history_length)
@property
def t_history(self): return self.history("date time",count=self.history_length)
@property
def x_samples(self): return self.history("x",count=self.average_samples)
@property
def y_samples(self): return self.history("y",count=self.average_samples)
@property
def last_image_timestamp(self):
t = self.history("image_timestamp",count=1)
t = t[0] if len(t)>0 else 0
return t
def get_x_control(self): return tofloat(caget(self.x_read_PV))
def set_x_control(self,value): return caput(self.x_PV,value)
x_control = property(get_x_control,set_x_control)
def get_y_control(self): return tofloat(caget(self.y_read_PV))
def set_y_control(self,value): return caput(self.y_PV,value)
y_control = property(get_y_control,set_y_control)
def get_x_control_average(self): return average(self.x_control_samples)
def set_x_control_average(self,value): self.x_control = value
x_control_average = property(get_x_control_average,set_x_control_average)
def get_y_control_average(self): return average(self.y_control_samples)
def set_y_control_average(self,value): self.y_control = value
y_control_average = property(get_y_control_average,set_y_control_average)
@property
def x_control_samples(self):
return self.history("x_control",count=self.average_samples)
@property
def y_control_samples(self):
return self.history("y_control",count=self.average_samples)
@property
def x_control_history(self):
return self.history("x_control",count=self.history_length)
@property
def y_control_history(self):
return self.history("y_control",count=self.history_length)
@property
def x_control_corrected(self):
"""Value for the y control in roder to bring the y position back to
its nominal value"""
x_control = self.x_control_average - \
(self.x_average - self.x_nominal)*self.x_gain
return x_control
@property
def y_control_corrected(self):
"""Value for the y control in roder to bring the y position back to
its nominal value"""
y_control = self.y_control_average - \
(self.y_average - self.y_nominal)*self.y_gain
return y_control
def apply_correction(self):
self.apply_x_correction()
self.apply_y_correction()
def apply_x_correction(self):
if self.image_OK:
self.x_control = self.x_control_corrected
def apply_y_correction(self):
if self.image_OK:
self.y_control = self.y_control_corrected
@property
def x_beam(self): return self.beam_position[0]
@property
def y_beam(self): return self.beam_position[1]
@property
def beam_position_HyunSun(self):
from transmissive_beamstop import beam_center
x,y = beam_center(self.image)
return x,y
@property
def beam_position(self):
xprofile,yprofile = xy_projections(self.image,self.ROI_center,self.ROI_width)
x,y = CFWHM(xprofile),CFWHM(yprofile)
return x,y
@property
def ROI_center(self): return self.x_ROI_center,self.y_ROI_center
@property
def image_OK(self):
if self.image_overloaded: OK = False
elif self.SNR < self.min_SNR: OK = False
elif self.analysis_filter not in self.image_basename: OK = False
else: OK = True
return OK
@property
def image_overloaded(self):
return overloaded_pixels(self.image,self.ROI_center,self.ROI_width)
@property
def SNR(self):
xprofile,yprofile = xy_projections(self.image,self.ROI_center,self.ROI_width)
return (SNR(xprofile)+SNR(yprofile))/2
@property
def image(self):
from numimage import numimage
from numpy import uint16
filename = self.image_filename
if filename: image = numimage(filename)
else: image = self.default_image
return image
@property
def default_image(self):
from numimage import numimage
from numpy import uint16
image = numimage((3840,3840),pixelsize=0.0886,dtype=uint16)+10
return image
@property
def image_timestamp(self):
"""Full pathname of the last recorded image"""
from os.path import getmtime
from normpath import normpath
filename = self.image_filename
t = getmtime(normpath(filename)) if filename else 0
return t
@property
def image_filename(self):
"""Full pathname of the last recorded image"""
image_filenames = self.image_filenames
if len(image_filenames)>0: image_filename = image_filenames[-1]
else: image_filename = ""
self.last_image_filename = image_filename
return image_filename
last_image_filename = ""
@property
def image_filenames(self):
"""Full pathnames of the last recorded images"""
from rayonix_detector_continuous import ccd
return ccd.image_filenames
@property
def image_basename(self):
"""Filename of the last recorded image, with out directory"""
from os.path import basename
return basename(self.image_filename)
def history(self,name,count):
"""Log history filtered by image filename pattern"""
from numpy import array,chararray
filename = self.log.history("filename",count=count)
values = self.log.history(name,count=count)
filename = array(filename,str).view(chararray)
match = filename.find(self.history_filter)>=0
values = array(values)[match]
return values
class ClusterGroup(object):
"""
A Group of word cluster, representing the unique log types within a logfile
"""
Args = ""
Log = ""
VarThreshold = 10 #How many siblings a string node must have before it is considered to be variable data
VarDistance = 20
rootNode = ClusterNode(NodeContent="ROOTNODE")
entries = []
def __init__(self, args):
self.rootNode = ClusterNode(NodeContent="ROOTNODE")
self.Args = args
def IsMatch(self, logline):
'''
Test the incoming log line to see if it matches this clustergroup
Return boolean match
'''
logwords = commonvars.FindCommonRegex(logline).split()
#TODO Split at '=' marks as well
currentNode = self.rootNode
for logword in logwords: #process logs a word at a time
#match our own children first
match = currentNode.MatchChild(MatchContent=logword)
if match == None: #then try our siblings
match = currentNode.MatchNephew(MatchContent=logword)
if match == None: #then add a new child
match = currentNode.AddChild(NodeContent=logword)
if match == None:
print "FAILED"
else:
currentNode = match
def IsEndNode(self, Node):
'''
Is This Node the final word of a log template?
@return: True or False
'''
endnode = False
hasNephews = False
if (len(Node.Children) is
0): #I'm an EndNode for a log wording cluster
if Node.Parent is not None: #let's make sure our siblings are all endnodes too, and this is really var data
for sibling in Node.Parent.Children:
if len(sibling.Children) > 0:
hasNephews = True
if (hasNephews is False) and (len(
Node.Parent.Children) >= ClusterGroup.VarThreshold
): #log event ends in a variable
endnode = True
if (hasNephews is
False) and (len(Node.Parent.Children)
== 1): #log event ends in a fixed string
endnode = True
if endnode is True:
entry = Node.GeneratePath()
if entry not in self.entries:
self.entries.append(entry)
def BuildResultsTree(self, node):
'''
Recurse through the Node Tree, identifying and printing complete log patterns'
@return: None (recursive function)
'''
if self.IsEndNode(node) == True:
return None # no children so back up a level
for childnode in node.Children:
self.BuildResultsTree(childnode)
def Results(self):
'''
Display all identified unique log event types
@return None
'''
#if options.outfile == true: dump to file
print "\n========== Potential Unique Log Events ==========\n"
self.BuildResultsTree(self.rootNode)
#Todo - commandline args to toggle levenshtein identification of dupes
previous = ''
for entry in self.entries:
if levenshtein.levenshtein(entry,
previous) < ClusterGroup.VarDistance:
print "\t" + entry
else:
print entry
previous = entry
def Run(self):
try:
self.Log = LogFile(self.Args.logfile)
except IOError:
print "File: " + self.Log.Filename + " cannot be opened : " + str(
sys.exc_info()[1])
#TODO: log to stderr
raise IOError()
#if args.v > 0 : print "Processing Log File " + log.Filename + ":" + str(log.Length) + " bytes"
logline = self.Log.RetrieveCurrentLine()
widgets = [
'Processing potential messages: ',
progressbar.Percentage(), ' ',
progressbar.Bar(marker=progressbar.RotatingMarker()), ' ',
progressbar.ETA()
]
if self.Args.quiet is False:
pbar = progressbar.ProgressBar(widgets=widgets, maxval=100).start()
while logline != "": #TODO: Make this actually exit on EOF
self.IsMatch(logline)
if self.Args.quiet is False:
pbar.update((1.0 * self.Log.Position / self.Log.Length) * 100)
logline = self.Log.RetrieveCurrentLine()
if self.Args.quiet is False: pbar.finish()
def GenPlugin(self):
'''
Create a Template OSSIM agent plugin file using the identified log templates as SIDs
@return: The filename of the generated plugin
'''
generator = plugingenerate.Generator(self.entries)
generator.WritePlugin()
return generator.PluginFile
def handle_request(self):
"""Web server function."""
host = request.args.get('host')
mac = request.args.get('mac')
tab = request.args.get('tab')
request_json = request.get_json()
Debug.debug_print(3, "request_json: " + pprint.pformat(request_json))
try:
message = request.path
if request.path == self.WEB_GUI_PATH:
settings = self.render_settings_html()
active_tab = 'about'
if tab is not None:
active_tab = tab
result = render_template(
'index.html', settings=settings, active_tab=active_tab,
restart_ping_path=Settings.WEB_API_PATH + 'restart_ping',
poweron_path=Settings.WEB_API_PATH + 'poweron',
poweroff_path=Settings.WEB_API_PATH + 'poweroff')
elif request.path == self.WEB_API_PATH + 'poweron':
message = 'poweron: mac={}'
message = message.format(str(mac))
result = self._poweron()
elif request.path == self.WEB_API_PATH + 'poweroff':
message = 'poweroff: host={}'
message = message.format(str(host))
result = self._poweroff()
elif request.path == self.WEB_API_PATH + 'restart_ping':
message = 'restart_ping'
result = self._restart_ping()
elif request.path == self.WEB_API_PATH + 'save_settings':
message = 'save_settings'
result = self._save_settings(request_json)
elif request.path == self.WEB_API_PATH + 'delete_param_value':
param = None
value = None
if 'param' in request_json:
param = request_json['param']
if 'value' in request_json:
value = request_json['value']
message = 'delete_param_value: param={}, value={}'
message = message.format(param, value)
result = self._delete_param_value(param, value)
elif request.path == self.WEB_API_PATH + 'add_param_value':
param = None
if 'param' in request_json:
param = request_json['param']
if 'value' in request_json:
value = request_json['value']
message = 'add_param_value: param={}, value={}'
message = message.format(param, value)
result = self._add_param_value(param, value)
except:
error_log = LogFile(self.ERROR_LOG)
error_log.write([message])
traceback_message = traceback.format_exc()
error_log.write([traceback_message], date_time=False)
if Debug.debug > 0:
Debug.debug_print(1, traceback_message)
return self._json_response(traceback_message, 500)
return self._json_response('Internal system error!', 500)
message_log = LogFile(self.MESSAGE_LOG)
message_log.write([message])
return result
def setUp(self):
self.logfile = LogFile(self.LOGPATH, self.JOBPATH, self.JOB)
class Xray_Beam_Check(object):
name = "xray_beam_check"
class Settings(object):
name = "xray_beam_check.settings"
# X-Ray beam steering controls.
# Horizontal deflection mirror jacks
def get_x1_motor(self):
return MirrorH.m1.prefix
def set_x1_motor(self, value):
MirrorH.m1.prefix = value
x1_motor = property(get_x1_motor, set_x1_motor)
def get_x2_motor(self):
return MirrorH.m2.prefix
def set_x2_motor(self, value):
MirrorH.m2.prefix = value
x2_motor = property(get_x2_motor, set_x2_motor)
def get_y_motor(self):
return MirrorV.prefix
def set_y_motor(self, value):
MirrorV.prefix = value
y_motor = property(get_y_motor, set_y_motor)
dx_scan = persistent_property(
"dx_scan", 6 * 0.000416 * 2 /
1.045) # stepsize: 0.000416*2/1.045 = 0.000796 mrad
dy_scan = persistent_property("dy_scan", 0.150) # in V
x_resolution = persistent_property(
"x_resolution",
0.000416 * 2 / 1.045) # stepsize: 0.000416*2/1.045 = 0.000796 mrad
y_resolution = persistent_property("y_resolution", 0.001) # in V
beamline_mode = persistent_property("beamline_mode", "SAXS/WAXS")
beamline_modes = ["SAXS/WAXS", "Laue"]
@property
def x_aperture_control(self):
"""Which motor to use to narrow down the horizontal arperture"""
return s1hg if self.beamline_mode == "Laue" else shg
@property
def y_aperture_control(self):
"""Which motor to use to narrow down the horizontal arperture"""
return svg
# To narrow down aperture upstream of the detector for higher senitivity
def get_x_aperture_motor(self):
return self.x_aperture_control.prefix
def set_x_aperture_motor(self, value):
self.x_aperture_control.prefix = value
x_aperture_motor = property(get_x_aperture_motor, set_x_aperture_motor)
def get_y_aperture_motor(self):
return self.y_aperture_control.prefix
def set_y_aperture_motor(self, value):
self.y_aperture_control.prefix = value
y_aperture_motor = property(get_y_aperture_motor, set_y_aperture_motor)
x_aperture_norm = persistent_property("x_aperture_norm", 0.150)
y_aperture_norm = persistent_property("y_aperture_norm", 0.050)
x_aperture_scan = persistent_property("x_aperture_scan", 0.050)
y_aperture_scan = persistent_property("y_aperture_scan", 0.020)
def get_x_aperture(self):
return self.x_aperture_control.command_value
def set_x_aperture(self, value):
self.x_aperture_control.command_value = value
x_aperture = property(get_x_aperture, set_x_aperture)
def get_y_aperture(self):
return self.y_aperture_control.command_value
def set_y_aperture(self, value):
self.y_aperture_control.command_value = value
y_aperture = property(get_y_aperture, set_y_aperture)
@property
def x_aperture_moving(self):
return self.x_aperture_control.moving
@property
def y_aperture_moving(self):
return self.y_aperture_control.moving
def get_timing_system_ip_address(self):
return timing_system.ip_address
def set_timing_system_ip_address(self, value):
timing_system.ip_address = value
timing_system_ip_address = property(get_timing_system_ip_address,
set_timing_system_ip_address)
def get_scope_ip_address(self):
return xray_pulse.scope.ip_address
def set_scope_ip_address(self, value):
xray_pulse.scope.ip_address = value
scope_ip_address = property(get_scope_ip_address, set_scope_ip_address)
ms_on_norm = persistent_property("ms_on_norm", True)
xosct_on_norm = persistent_property("xosct_on_norm", True)
scan_timeout = 30 # seconds
timing_mode = persistent_property("timining_mode", "SAXS/WAXS")
timing_modes = ["SAXS/WAXS", "Laue"]
@property
def timing_sequencer(self):
return timing_sequencer if self.timing_mode == "Laue" \
else Ensemble_SAXS
settings = Settings()
log = LogFile(name + ".log", ["date time", "x_control", "y_control"])
if log.filename == "":
log.filename = "//mx340hs/data/anfinrud_1703/Logfiles/xray_beam_check.log"
x_scan_x = persistent_property("x_scan_x", [])
x_scan_I = persistent_property("x_scan_I", [])
x_scan_sigI = persistent_property("x_scan_sigI", [])
y_scan_y = persistent_property("y_scan_y", [])
y_scan_I = persistent_property("y_scan_I", [])
y_scan_sigI = persistent_property("y_scan_sigI", [])
cancelled = persistent_property("cancelled", False)
x_scan_started = persistent_property("x_scan_started", 0.0)
y_scan_started = persistent_property("y_scan_started", 0.0)
def get_x_control(self):
return MirrorH.command_value
def set_x_control(self, value):
MirrorH.command_value = value
x_control = property(get_x_control, set_x_control)
def x_next(self, x):
"""The next value that is an intergal motor step"""
offset = MirrorH.offset
dx = self.settings.x_resolution
return round_next(x - offset, dx) + offset
def y_next(self, y):
"""The next value that is an integral motor step"""
offset = 0 ##MirrorV.offset
dy = self.settings.y_resolution
return round_next(y - offset, dy) + offset
def get_y_control(self):
return MirrorV.command_value
def set_y_control(self, value):
MirrorV.command_value = value
y_control = property(get_y_control, set_y_control)
def x_pre_scan_setup(self):
self.settings.x_aperture_norm = self.settings.x_aperture
self.settings.x_aperture = self.settings.x_aperture_scan
while self.settings.x_aperture_moving and not self.cancelled:
sleep(0.1)
##xray_pulse.scope.sampling_mode = "RealTime" # Lauecollect uses "Sequence"
xray_pulse.enabled = True
def x_post_scan_setup(self):
self.settings.x_aperture = self.settings.x_aperture_norm
xray_pulse.enabled = False
def y_pre_scan_setup(self):
self.settings.y_aperture_norm = self.settings.y_aperture
self.settings.y_aperture = self.settings.y_aperture_scan
while self.settings.y_aperture_moving and not self.cancelled:
sleep(0.1)
##xray_pulse.scope.sampling_mode = "RealTime" # Lauecollect uses "Sequence"
xray_pulse.enabled = True
def y_post_scan_setup(self):
self.settings.y_aperture = self.settings.y_aperture_norm
xray_pulse.enabled = False
def timing_system_pre_scan_setup(self):
# Save current settings
self.settings.xosct_on_norm = self.settings.timing_sequencer.xosct_on
self.settings.ms_on_norm = self.settings.timing_sequencer.ms_on
if not self.settings.timing_sequencer.xosct_on:
self.settings.timing_sequencer.xosct_on = True
if not self.settings.timing_sequencer.ms_on:
self.settings.timing_sequencer.ms_on = True
while not (self.settings.timing_sequencer.xosct_on and self.settings.
timing_sequencer.ms_on) and not self.cancelled:
sleep(0.1)
def timing_system_post_scan_setup(self):
# Restore settings
self.settings.timing_sequencer.xosct_on = self.settings.xosct_on_norm
self.settings.timing_sequencer.ms_on = self.settings.ms_on_norm
def get_x_scan_running(self):
return self.x_scan_started > time() - self.settings.scan_timeout
def set_x_scan_running(self, value):
if value:
if not self.x_scan_running: self.start_x_scan()
else: self.cancelled = True
x_scan_running = property(get_x_scan_running, set_x_scan_running)
def get_y_scan_running(self):
return self.y_scan_started > time() - self.settings.scan_timeout
def set_y_scan_running(self, value):
if value:
if not self.y_scan_running: self.start_y_scan()
else: self.cancelled = True
y_scan_running = property(get_y_scan_running, set_y_scan_running)
def start_x_scan(self):
self.cancelled = False
start_new_thread(self.perform_x_scan, ())
def start_y_scan(self):
self.cancelled = False
start_new_thread(self.perform_y_scan, ())
def perform_x_scan(self):
self.x_scan_started = time()
self.x_pre_scan_setup()
self.timing_system_pre_scan_setup()
self.x_scan_x = []
self.x_scan_I = []
self.x_scan_sigI = []
x0 = self.x_control
# Start scanning in positive direction.
dx = self.settings.dx_scan
x = x0
self.x_control = x
I, sigI = self.I_sigI
self.x_scan_x += [x]
self.x_scan_I += [I]
self.x_scan_sigI += [sigI]
x += dx
self.x_control = x
I, sigI = self.I_sigI
self.x_scan_x += [x]
self.x_scan_I += [I]
self.x_scan_sigI += [sigI]
# If the intensity goes down, reverse direction.
if self.x_scan_I[1] < self.x_scan_I[0]:
dx = -dx
x = x0
self.x_scan_x = self.x_scan_x[::-1]
self.x_scan_I = self.x_scan_I[::-1]
self.x_scan_sigI = self.x_scan_sigI[::-1]
x += dx
self.x_control = x
I, sigI = self.I_sigI
self.x_scan_x += [x]
self.x_scan_I += [I]
self.x_scan_sigI += [sigI]
# Continue scanning until a maximum is reached.
while self.x_scan_I[-1] > self.x_scan_I[-2] and not self.cancelled:
x += dx
self.x_control = x
I, sigI = self.I_sigI
self.x_scan_x += [x]
self.x_scan_I += [I]
self.x_scan_sigI += [sigI]
# Return to the starting point.
self.x_control = x0
self.x_post_scan_setup()
self.timing_system_post_scan_setup()
self.x_scan_started = 0
def perform_y_scan(self):
self.y_scan_started = time()
self.y_pre_scan_setup()
self.timing_system_pre_scan_setup()
self.y_scan_y = []
self.y_scan_I = []
self.y_scan_sigI = []
y0 = self.y_control
# Start scanning in positive direction.
dy = self.settings.dy_scan
y = y0
self.y_control = y
I, sigI = self.I_sigI
self.y_scan_y += [y]
self.y_scan_I += [I]
self.y_scan_sigI += [sigI]
y += dy
self.y_control = y
I, sigI = self.I_sigI
self.y_scan_y += [y]
self.y_scan_I += [I]
self.y_scan_sigI += [sigI]
# If the intensity goes down, reverse direction.
if self.y_scan_I[1] < self.y_scan_I[0]:
dy = -dy
y = y0
self.y_scan_y = self.y_scan_y[::-1]
self.y_scan_I = self.y_scan_I[::-1]
self.y_scan_sigI = self.y_scan_sigI[::-1]
y += dy
self.y_control = y
I, sigI = self.I_sigI
self.y_scan_y += [y]
self.y_scan_I += [I]
self.y_scan_sigI += [sigI]
# Continue scanning until a mayimum is reached.
while self.y_scan_I[-1] > self.y_scan_I[-2] and not self.cancelled:
y += dy
self.y_control = y
I, sigI = self.I_sigI
self.y_scan_y += [y]
self.y_scan_I += [I]
self.y_scan_sigI += [sigI]
# Return to the starting point.
self.y_control = y0
self.y_post_scan_setup()
self.timing_system_post_scan_setup()
self.y_scan_started = 0
@property
def x_control_corrected(self):
if len(self.x_scan_x) < 3 or len(self.x_scan_I) < 3: return nan
x = parabola_vertex(self.x_scan_x[-3:], self.x_scan_I[-3:])[0]
x = self.x_next(x)
return x
@property
def y_control_corrected(self):
if len(self.y_scan_y) < 3 or len(self.y_scan_I) < 3: return nan
y = parabola_vertex(self.y_scan_y[-3:], self.y_scan_I[-3:])[0]
##y = self.y_next(y)
return y
@property
def x_scan_x_fit(self):
return parabolic_fit(self.x_scan_x, self.x_scan_I)[0]
@property
def x_scan_I_fit(self):
return parabolic_fit(self.x_scan_x, self.x_scan_I)[1]
@property
def y_scan_y_fit(self):
return parabolic_fit(self.y_scan_y, self.y_scan_I)[0]
@property
def y_scan_I_fit(self):
return parabolic_fit(self.y_scan_y, self.y_scan_I)[1]
def apply_x_correction(self):
self.x_control = self.x_control_corrected
self.update_log()
def apply_y_correction(self):
self.y_control = self.y_control_corrected
self.update_log()
def update_log(self):
"""Create a log file entry every time a correction is applied"""
self.log.log(self.x_control, self.y_control)
@property
def I_sigI(self):
"""X-ray beam intensity"""
xray_pulse.reset_average()
sleep(4)
I = xray_pulse.average
sI = xray_pulse.stdev
N = xray_pulse.count
sigI = I / sqrt(N - 1) if N > 1 else nan
return I, sigI
class Xray_Beam_Position_Check(object):
name = "xray_beam_position_check"
class Settings(object):
name = "settings"
# X-Ray beam steering controls.
# Horizontal deflection mirror jacks
def get_x1_motor(self):
return MirrorH.m1.prefix
def set_x1_motor(self, value):
MirrorH.m1.prefix = value
x1_motor = property(get_x1_motor, set_x1_motor)
def get_x2_motor(self):
return MirrorH.m2.prefix
def set_x2_motor(self, value):
MirrorH.m2.prefix = value
x2_motor = property(get_x2_motor, set_x2_motor)
def get_y_motor(self):
return MirrorV.prefix
def set_y_motor(self, value):
MirrorV.prefix = value
y_motor = property(get_y_motor, set_y_motor)
# To narrow down aperture upstream of the detector for higher senitivity
def get_x_aperture_motor(self):
return shg.prefix
def set_x_aperture_motor(self, value):
shg.prefix = value
x_aperture_motor = property(get_x_aperture_motor, set_x_aperture_motor)
def get_y_aperture_motor(self):
return svg.prefix
def set_y_aperture_motor(self, value):
svg.prefix = value
y_aperture_motor = property(get_y_aperture_motor, set_y_aperture_motor)
x_aperture_norm = persistent_property("x_aperture_norm", 0.150)
y_aperture_norm = persistent_property("y_aperture_norm", 0.050)
x_aperture_scan = persistent_property("x_aperture_scan", 0.050)
y_aperture_scan = persistent_property("y_aperture_scan", 0.020)
def get_x_aperture(self):
return shg.command_value
def set_x_aperture(self, value):
shg.command_value = value
x_aperture = property(get_x_aperture, set_x_aperture)
def get_y_aperture(self):
return svg.command_value
def set_y_aperture(self, value):
svg.command_value = value
y_aperture = property(get_y_aperture, set_y_aperture)
def get_timing_system_ip_address(self):
return timing_system.ip_address
def set_timing_system_ip_address(self, value):
timing_system.ip_address = value
timing_system_ip_address = property(get_timing_system_ip_address,
set_timing_system_ip_address)
acquire_image_timeout = 30 # seconds
x_gain = persistent_property("x_gain", 0.143) # mrad/mm
y_gain = persistent_property("y_gain", 2.7) # V/mm was: 1/3.3e-3
x_nominal = persistent_property("x_nominal",
175.927) # mm from left, 2016-03-05
y_nominal = persistent_property("y_nominal",
174.121) # mm from top, 2016-03-05
history_length = persistent_property("history_length", 50)
average_samples = persistent_property("average_samples", 1)
x_enabled = persistent_property("x_enabled", False)
y_enabled = persistent_property("y_enabled", False)
ROI_width = persistent_property("ROI_width", 1.0) # mm
x_ROI_center = persistent_property("x_ROI_center",
175.9) # mm from left
y_ROI_center = persistent_property("y_ROI_center",
174.1) # mm from top
min_SNR = persistent_property("min_SNR", 5.0) # signal-to-noise ratio
image_filename = persistent_property(
"image_filename",
"//mx340hs/data/rayonix_scratch/xray_beam_position.rx")
settings = Settings()
log = LogFile(
name + ".log",
["date time", "x", "y", "x_control", "y_control", "image_timestamp"])
if log.filename == "":
log.filename = "//mx340hs/data/anfinrud_1611/Logfiles/xray_beam_position_check.log"
def update(self):
t = self.image_timestamp
if t != 0 and abs(t - self.last_image_timestamp) >= 0.1:
x, y = self.beam_position
xc, yc = self.x_control, self.y_control
self.log.log(x, y, xc, yc, t)
@property
def x_average(self):
return average(self.x_samples)
@property
def y_average(self):
return average(self.y_samples)
@property
def x_history(self):
return self.log.history("x", count=self.settings.history_length)
@property
def y_history(self):
return self.log.history("y", count=self.settings.history_length)
@property
def t_history(self):
return self.log.history("date time",
count=self.settings.history_length)
@property
def x_samples(self):
return self.log.history("x", count=self.settings.average_samples)
@property
def y_samples(self):
return self.log.history("y", count=self.settings.average_samples)
@property
def last_image_timestamp(self):
t = self.log.history("image_timestamp", count=1)
t = t[0] if len(t) > 0 else 0
return t
def get_x_control(self):
return tofloat(caget(self.x_read_PV))
def set_x_control(self, value):
return caput(self.x_PV, value)
x_control = property(get_x_control, set_x_control)
def get_y_control(self):
return tofloat(caget(self.y_read_PV))
def set_y_control(self, value):
return caput(self.y_PV, value)
y_control = property(get_y_control, set_y_control)
def get_x_control_average(self):
return average(self.x_control_samples)
def set_x_control_average(self, value):
self.x_control = value
x_control_average = property(get_x_control_average, set_x_control_average)
def get_y_control_average(self):
return average(self.y_control_samples)
def set_y_control_average(self, value):
self.y_control = value
y_control_average = property(get_y_control_average, set_y_control_average)
@property
def x_control_samples(self):
return self.log.history("x_control",
count=self.settings.average_samples)
@property
def y_control_samples(self):
return self.log.history("y_control",
count=self.settings.average_samples)
@property
def x_control_history(self):
return self.log.history("x_control",
count=self.settings.history_length)
@property
def y_control_history(self):
return self.log.history("y_control",
count=self.settings.history_length)
@property
def x_control_corrected(self):
"""Value for the y control in order to bring the x position back to
its nominal value"""
x_control = self.x_control_average - \
(self.x_average - self.x_nominal)*self.settings.x_gain
return x_control
@property
def y_control_corrected(self):
"""Value for the y control in order to bring the y position back to
its nominal value"""
y_control = self.y_control_average - \
(self.y_average - self.y_nominal)*self.settings.y_gain
return y_control
def apply_correction(self):
self.apply_x_correction()
self.apply_y_correction()
def apply_x_correction(self):
self.x_control = self.x_control_corrected
def apply_y_correction(self):
self.y_control = self.y_control_corrected
cancelled = persistent_property("cancelled", False)
acquire_image_started = persistent_property("acquire_image_started", 0.0)
def get_x_control(self):
return MirrorH.command_value
def set_x_control(self, value):
MirrorH.command_value = value
x_control = property(get_x_control, set_x_control)
def x_next(self, x):
"""The next value that is an intergal motor step"""
offset = MirrorH.offset
dx = self.settings.x_resolution
return round_next(x - offset, dx) + offset
def y_next(self, y):
"""The next value that is an intergal motor step"""
offset = 0 ##MirrorV.offset
dy = self.settings.y_resolution
return round_next(y - offset, dy) + offset
def get_y_control(self):
return MirrorV.command_value
def set_y_control(self, value):
MirrorV.command_value = value
y_control = property(get_y_control, set_y_control)
def acquire_image_setup(self):
self.settings.x_aperture = self.settings.x_aperture_scan
self.settings.y_aperture = self.settings.y_aperture_scan
def acquire_image_unsetup(self):
self.settings.x_aperture = self.settings.x_aperture_norm
self.settings.y_aperture = self.settings.y_aperture_norm
def get_acquire_image_running(self):
return self.acquire_image_started > time(
) - self.settings.acquire_image_timeout
def set_acquire_image_running(self, value):
if value:
if not self.acquire_image_running: self.start_acquire_image()
else: self.cancelled = True
acquire_image_running = property(get_acquire_image_running,
set_acquire_image_running)
def start_acquire_image(self):
self.cancelled = False
start_new_thread(self.acquire_image, ())
def acquire_image(self):
self.acquire_image_started = time()
self.acquire_image_setup()
ccd.ignore_first_trigger = False
ccd.acquire_images_triggered([normpath(self.settings.image_filename)])
show_images(normpath(self.settings.image_filename))
Ensemble_SAXS.acquire(delays=[0], laser_on=[False])
tmax = time() + self.settings.acquire_image_timeout
while ccd.state() != "idle" and not self.cancelled and time() < tmax:
sleep(0.05)
ccd.abort()
self.acquire_image_unsetup()
self.acquire_image_started = 0
self.update()
@property
def x_beam(self):
return self.beam_position[0]
@property
def y_beam(self):
return self.beam_position[1]
@property
def beam_position(self):
xprofile, yprofile = xy_projections(self.image, self.ROI_center,
self.ROI_width)
x, y = CFWHM(xprofile), CFWHM(yprofile)
return x, y
@property
def x_error(self):
return self.x_beam - self.x_nominal
@property
def y_error(self):
return self.y_beam - self.y_nominal
@property
def image_OK(self):
return not self.image_overloaded and self.SNR > self.settings.min_SNR
@property
def image_overloaded(self):
return overloaded_pixels(self.image, self.ROI_center, self.ROI_width)
@property
def SNR(self):
xprofile, yprofile = xy_projections(self.image, self.ROI_center,
self.ROI_width)
return (SNR(xprofile) + SNR(yprofile)) / 2
@property
def image(self):
from numimage import numimage
filename = normpath(self.settings.image_filename)
if exists(filename): image = numimage(filename)
else: image = self.default_image
# Needed for "BeamProfile" to detect image updates.
# If a memory-mapped image would be chached by "BeamProfile", the
# comparison with the new image would show no difference, since the
# cached image dynamically updates.
image = image.copy()
return image
@property
def x_ROI_center(self):
return self.settings.x_ROI_center
@property
def y_ROI_center(self):
return self.settings.y_ROI_center
@property
def ROI_center(self):
return self.x_ROI_center, self.y_ROI_center
@property
def ROI_width(self):
return self.settings.ROI_width
@property
def x_nominal(self):
return self.settings.x_nominal
@property
def y_nominal(self):
return self.settings.y_nominal
@property
def default_image(self):
from numimage import numimage
from numpy import uint16
image = numimage((3840, 3840), pixelsize=0.0886, dtype=uint16) + 10
return image
@property
def image_timestamp(self):
"""Full pathname of the last recorded image"""
from os.path import getmtime, dirname
from os import listdir
filename = normpath(self.settings.image_filename)
if exists(filename):
listdir(dirname(filename)) # for NFS attibute caching
t = getmtime(filename) if exists(filename) else 0
return t
