def runWrappedExtendedSyntaxCommandAndReturnException(self, command):
'''(time, e) = runWrappedExtendedSyntaxCommandAndCollectAnyException(command)
NOTE: pickle won't pickle-up exc_info() output from in here for some reason.
Returns the exception instead.'''
wrappedCommand = """
import pickle
import sys
from time import clock
def trySomething():
try:
unlikelyName8466_t = clock()
%s
unlikelyName8466_t = clock() - unlikelyName8466_t
except (Exception, java.lang.Exception), unlikelyName8466_exception:
print '* returning: ', unlikelyName8466_exception, '*'
return pickle.dumps((None, unlikelyName8466_exception))
return pickle.dumps((unlikelyName8466_t, None))
""" % command
JythonServerFacade.getInstance().runCommand(wrappedCommand)
sleep(.1)
mystdout = ExtendedSyntaxCommandTest.FileLikeObject()
mystderr = ExtendedSyntaxCommandTest.FileLikeObject()
saveout = sys.stdout
saveerr = sys.stderr
sys.stdout = mystdout
sys.stderr = mystderr
try:
pickledTuple = JythonServerFacade.getInstance().evaluateCommand("trySomething()") #just an exception for now
except (Exception, java.lang.Exception), e:
sys.stdout = saveout
sys.stderr = saveerr
raise e
def runWrappedExtendedSyntaxCommandAndReturnException(self, command):
'''(time, e) = runWrappedExtendedSyntaxCommandAndCollectAnyException(command)
NOTE: pickle won't pickle-up exc_info() output from in here for some reason.
Returns the exception instead.'''
wrappedCommand = """
import pickle
import sys
from time import clock
def trySomething():
try:
unlikelyName8466_t = clock()
%s
unlikelyName8466_t = clock() - unlikelyName8466_t
except (Exception, java.lang.Exception), unlikelyName8466_exception:
print '* returning: ', unlikelyName8466_exception, '*'
return pickle.dumps((None, unlikelyName8466_exception))
return pickle.dumps((unlikelyName8466_t, None))
""" % command
JythonServerFacade.getInstance().runCommand(wrappedCommand)
sleep(.1)
mystdout = ExtendedSyntaxCommandTest.FileLikeObject()
mystderr = ExtendedSyntaxCommandTest.FileLikeObject()
saveout = sys.stdout
saveerr = sys.stderr
sys.stdout = mystdout
sys.stderr = mystderr
try:
pickledTuple = JythonServerFacade.getInstance().evaluateCommand(
"trySomething()") #just an exception for now
except (Exception, java.lang.Exception), e:
sys.stdout = saveout
sys.stderr = saveerr
raise e
def pulse(*args, **kwargs):
''' send pulse sweep generated by Keithley 2461 to the sample via Synapse Switch Box.
This command takes only 6 or 8 input parameters:
The first 2 (in 6 parameters case) or 4 (in 8 parameters case) parameters defines the contact points in the Synapse Switch Box;
The last 4 parameters defines pulse sweep to be generated by the Keithley 2461.
Command syntax:
pulse source_high source_low current width timeDelay numberOfPulses
for 6 input parameters
pulse source_1_high source_2_high source_1_low source_2_low current width timeDelay numberOfPulses
for 8 input parameters
'''
if len(args) == 6:
if args[0]==args[1]:
raise Exception("Cannot use the same Synapse terminal for both high and low.")
synapse_setall.rawAsynchronousMoveTo("Open circuit")
#configure synapse
synapseHigh = whichSynapseTerminal(args[0])
synapseHigh.rawAsynchronousMoveTo("Source high")
synapseLow = whichSynapseTerminal(args[1])
synapseLow.rawAsynchronousMoveTo("Source low")
sleep(1) #ensure above finished before statement below
if kwargs.get('KEITHLEY_SOURCE_MODE', curr) == curr or str(JythonServerFacade.getInstance().getFromJythonNamespace('KEITHLEY_SOURCE_MODE')) == curr:
generateCurrentPulseFromKeithley(args[2], args[3], args[4]/2, args[5])
elif kwargs.get('KEITHLEY_SOURCE_MODE', curr) == volt or str(JythonServerFacade.getInstance().getFromJythonNamespace('KEITHLEY_SOURCE_MODE')) == volt:
generateVoltagePulseFromKeithley(args[2], args[3], args[4]/2, args[5])
else:
raise Exception("Keithley source mode %s is not supported" % KEITHLEY_SOURCE_MODE)
synapse_setall.rawAsynchronousMoveTo("STV")
print "Pulse sweep completed."
elif len(args)== 8:
if len(args[:4])!=len(set(args[:4])):
raise Exception("Cannot use the same Synapse terminal more than once in this command.")
synapse_setall.rawAsynchronousMoveTo("Open circuit")
#configure synapse
synapseHigh1 = whichSynapseTerminal(args[0])
synapseHigh1.rawAsynchronousMoveTo("Source high")
synapseHigh2 = whichSynapseTerminal(args[1])
synapseHigh2.rawAsynchronousMoveTo("Source high")
synapseLow1 = whichSynapseTerminal(args[2])
synapseLow1.rawAsynchronousMoveTo("Source low")
synapseLow2 = whichSynapseTerminal(args[3])
synapseLow2.rawAsynchronousMoveTo("Source low")
sleep(1)#ensure above finished before statement below
if kwargs.get('KEITHLEY_SOURCE_MODE', curr) == curr or str(JythonServerFacade.getInstance().getFromJythonNamespace('KEITHLEY_SOURCE_MODE')) == curr:
generateCurrentPulseFromKeithley(args[4], args[5], args[6]/2, args[7])
elif kwargs.get('KEITHLEY_SOURCE_MODE', curr) == volt or str(JythonServerFacade.getInstance().getFromJythonNamespace('KEITHLEY_SOURCE_MODE')) == volt:
generateVoltagePulseFromKeithley(args[4], args[5], args[6]/2, args[7])
else:
raise Exception("Keithley source mode %s is not supported" % KEITHLEY_SOURCE_MODE)
synapse_setall.rawAsynchronousMoveTo("STV")
print "Pulse sweep completed."
else:
raise Exception("Number of parameters is wrong, require 6 or 8 arguments.")
def run(self):
'''rocking motion of the specified scannable during scan. This call must be non-blocking.'''
while(self.runThread):
if (JythonServerFacade.getInstance().getScanStatus() == JythonStatus.RUNNING):
if not self.pd.isBusy():
self.pd.asynchronousMoveTo(self.getUpperGdaLimits()[0])
if (JythonServerFacade.getInstance().getScanStatus() == JythonStatus.RUNNING):
if not self.pd.isBusy():
self.pd.asynchronousMoveTo(self.getLowerGdaLimits()[0])
def checkForAnglePause(self, npoints, start, end, step, collectionTime):
if (self.paused):
JythonServerFacade.getInstance().setScriptStatus(
JythonStatus.PAUSED)
while (self.paused):
try:
print 'Angle Scan paused - Awaiting resume'
java.lang.Thread.sleep(10000)
except lang.InterruptedException:
self.checkForAngleInterrupt(npoints, start, end, step,
collectionTime)
def run(self):
'''rocking motion of the specified scannable during scan. This call must be non-blocking.'''
while (self.runThread):
if (JythonServerFacade.getInstance().getScanStatus() ==
JythonStatus.RUNNING):
if not self.pd.isBusy():
self.pd.asynchronousMoveTo(self.getUpperGdaLimits()[0])
if (JythonServerFacade.getInstance().getScanStatus() ==
JythonStatus.RUNNING):
if not self.pd.isBusy():
self.pd.asynchronousMoveTo(self.getLowerGdaLimits()[0])
def checkForKScanPause(self, npoints, start, end, step, edgeEnergy, twoD,
kStartTime, kEndTime, kWeighting):
if (self.paused):
JythonServerFacade.getInstance().setScriptStatus(
JythonStatus.PAUSED)
while (self.paused):
try:
print 'K Scan Scan paused - Awaiting resume'
java.lang.Thread.sleep(10000)
except lang.InterruptedException:
self.checkForKScanInterrupt(npoints, start, end, step,
edgeEnergy, twoD, kStartTime,
kEndTime, kWeighting)
def __init__(self, filename):
self.__version__ = '1.00'
self.hplcFile = filename
self.bean = HplcSessionBean.createFromXML(filename)
finder = gda.factory.Finder.getInstance()
find = finder.find
self.shutter = find('shutter')
self.bsdiode = find('bsdiode')
self.sample_type = find('sample_type')
self.sampleName = find("samplename")
self.environment = find("sample_environment")
self.tfg = finder.listAllLocalObjects("gda.device.Timer")[0]
self.ncddetectors = finder.listAllLocalObjects(
"uk.ac.gda.server.ncd.detectorsystem.NcdDetectorSystem")[0]
self.jsf = JythonServerFacade.getInstance()
self.readout_time = 0.1
#CREATE A LOGGER
self.logger = logging.getLogger('HPLC')
self.logger.setLevel(logging.INFO)
formatter = logging.Formatter(
'%(asctime)s: %(levelname)s: %(module)s: %(message)s',
"[%Y-%m-%d %H:%M:%S]")
streamhandler = logging.StreamHandler()
streamhandler.setFormatter(formatter)
if len(self.logger.handlers) == 0:
self.logger.addHandler(streamhandler)
self.logger.info('HPLC class version ' + self.__version__ +
' was instantiated')
def waitWhileBusy(self):
if not self._operating_continuously:
if JythonServerFacade.getInstance().getScanStatus()==RUNNING:
# loop until okay
while not self._getStatusAndHandleChange():
# not okay
sleep(self.secondsBetweenChecks)
self._collectNewMonitorValue()
def checkForKScanInterrupt(self, npoints, start, end, step, edgeEnergy,
twoD, kStartTime, kEndTime, kWeighting):
#if(self.facade.getScanStatus()==0 and self.facade.getScriptStatus()==0):
if (self.interrupted):
print 'Stopping k scan:Writing out data taken'
# write the data we have so far and return
self.stopDetector()
self.writeKScanSummary(npoints, start, end, step, edgeEnergy, twoD,
kStartTime, kEndTime, kWeighting)
self.interrupted = Boolean(0)
self.paused = Boolean(0)
JythonServerFacade.getInstance().setScriptStatus(JythonStatus.IDLE)
scandata = Vector()
scandata.add("STOP")
self.controller.update(None, scandata)
self.mcontroller.update(None, scandata)
print 'Now the nasty bit: throw an exception to stop running'
raise lang.InterruptedException()
def getLastScanCommand(self):
#jsf=InterfaceProvider.getJythonNamespace()
jsf = JythonServerFacade.getInstance()
sdp = jsf.getLastScanDataPoint()
strCmd = "GDA command"
if isinstance(sdp, ScanDataPoint):
strCmd = sdp.getCommand()
return strCmd
def run(self): # print "Thread: " + self.getName() + " started" while (self.runThread): if (JythonServerFacade.getInstance().getScanStatus() == JythonStatus.RUNNING and self.currenttemp >= float(MAXTEMP)): JythonServerFacade.getInstance().pauseCurrentScan() print "Scan paused as temperature " + self.getName() +" returns: "+str(self.currenttemp) elif (JythonServerFacade.getInstance().getScanStatus() == JythonStatus.PAUSED and self.currenttemp <= float(MINTEMP)): print "Scan resumed as temperature " + self.getName() +" returns: "+str(self.currenttemp) JythonServerFacade.getInstance().resumeCurrentScan() sleep(10)
def getLastCommand(self):
#jsf=InterfaceProvider.getJythonNamespace()
jsf=JythonServerFacade.getInstance();
historyFilePath = LocalProperties.get("gda.jythonTerminal.commandHistory.path", jsf.getDefaultScriptProjectFolder());
historyFileName = os.path.join(historyFilePath, ".cmdHistory.txt")
if not os.path.exists(historyFileName):
print "No history found"
strCmd=''
else:
historyFile=open(historyFileName, 'r');
strCmd=( historyFile.readlines() )[-1];
historyFile.close();
#print "The last command is: " + strCmd;
return strCmd
def __init__(self, beanFile):
self.__version__ = '1.02'
finder = gda.factory.Finder.getInstance()
find = finder.find
self.simulate = False
self.holdsample = SAMPLE_HOLD
self.samplevolume = 35
self.beanFile = beanFile
self.bean = BSSCSessionBean.createFromXML(beanFile)
self.bssc = finder.listAllLocalObjects(
"uk.ac.gda.devices.bssc.BioSAXSSampleChanger")[0]
self.tfg = finder.listAllLocalObjects("gda.device.Timer")[0]
self.jsf = JythonServerFacade.getInstance()
self.detector = finder.listAllLocalObjects(
"uk.ac.gda.server.ncd.detectorsystem.NcdDetectorSystem")[0]
self.shutter = find("shutter")
self.bsscscannable = find("bsscscannable")
self.processing = find("bssc_proc")
#self.energy = float(find("dcm_energy").getPosition())
self.sampleConcentration = find("sample_concentration")
self.sampleName = find("samplename")
self.sample_type = find('sample_type')
self.sample_environment = find('sample_environment')
self.experiment_definition = gdaserver.experiment_definition
self.metashop = gdaserver.metashop
self.meta = GDAMetadataProvider.getInstance()
#need to remove hardcoding
find("sample_thickness").asynchronousMoveTo(1.6)
self.progresscounter = 0
self.overheadsteps = 5
self.stepspersample = 8
if self.simulate:
print "running in simulation mode"
self.scannables = [self.detector, self.bsscscannable]
else:
self.cam = gda.factory.Finder.getInstance().find("bsaxscam")
self.scannables = [self.detector, self.bsscscannable, self.cam]
currentVisit = GDAMetadataProvider.getInstance().getMetadataValue(
"visit")
self.totalSteps = self.overheadsteps + self.bean.getMeasurements(
).size() * self.stepspersample
def __init__(self, detectorList=None):
# EXAFS PANEL CODE
self.scannableNamesVector = Vector()
self.scannableNamesVector.add("dcm_mono")
self.detectorNamesVector = Vector()
self.detectorNamesVector.add("counterTimer01")
self.detectorNamesVector.add("counterTimer02")
self.controller = Finder.find("ExafsController")
self.mcontroller = Finder.find("MicroFocusController")
self.title = "TITLE"
self.condition1 = "CONDITION1"
self.condition2 = "CONDITION2"
self.condition3 = "CONDITION3"
# Script code
self.das = Finder.find("daserver")
self.ionchambers = SlaveCounterTimer()
self.converter = Finder.find("auto_mDeg_idGap_mm_converter")
self.windowValues = [[0, 4095]] * 9
self.windowName = 'ALL'
self.ionchamberData = []
self.mcaList = []
self.scalarList = []
self.runs = NumTracker("tmp")
self.runprefix = 'i18exafs'
self.runext = '.dat'
self.fileno = self.runs.getCurrentFileNumber() + 1
self.runs.incrementNumber()
self.datadir = InterfaceProvider.getPathConstructor(
).createFromProperty("gda.data.scan.datawriter.datadir")
self.datafilename = self.datadir + '/' + str(self.fileno) + self.runext
if (detectorList != None):
self.detectorMask = detectorList
else:
self.detectorMask = [1, 1, 1, 1, 1, 1, 1, 1, 1]
self.mcadir = self.datadir + '/mca/' + str(self.fileno) + '/'
self.mcarootname = self.mcadir + str(self.fileno)
if not os.path.isdir(self.mcadir):
os.mkdir(self.mcadir)
self.tag = 1
self.facade = JythonServerFacade.getInstance()
self.scanList = []
self.noOfRepeats = 1
self.noOfPoints = 0
def getPosition(self):
'''Pauses until status is okay'''
self.statusRemainedGoodSinceLastGetPosition = 1.0
# loop until okay (note that the count will have been triggered if count time was given)
if JythonServerFacade.getInstance().getScanStatus() == RUNNING:
while not self.getStatusAndReport():
# not okay
self.statusRemainedGoodSinceLastGetPosition = 0.0
sleep(self.secondsBetweenChecks)
if self.countTime != None:
self.__triggerCount(self.countTime) #
self.__waitForCountToComplete()
else: # scan not running
currentStatus = self.getStatus()
if not currentStatus: # bad
print "WaitBelowAndShutter not holding readback as no scan is running"
self.statusRemainedGoodSinceLastGetPosition = currentStatus
# now okay
return self.statusRemainedGoodSinceLastGetPosition
def __init__(self, beanFile):
self.__version__ = '1.02'
finder = gda.factory.Finder.getInstance()
find = finder.find
self.simulate = False
self.holdsample = SAMPLE_HOLD
self.samplevolume = 35
self.beanFile = beanFile
self.bean = BSSCSessionBean.createFromXML(beanFile)
self.bssc = finder.listAllLocalObjects("uk.ac.gda.devices.bssc.BioSAXSSampleChanger")[0]
self.tfg = finder.listAllLocalObjects("gda.device.Timer")[0]
self.jsf = JythonServerFacade.getInstance()
self.detector = finder.listAllLocalObjects("uk.ac.gda.server.ncd.detectorsystem.NcdDetectorSystem")[0]
self.shutter = find("shutter")
self.bsscscannable = find("bsscscannable")
self.processing = find("bssc_proc")
#self.energy = float(find("dcm_energy").getPosition())
self.sampleConcentration = find("sample_concentration")
self.sampleName = find("samplename")
self.sample_type = find('sample_type')
self.sample_environment = find('sample_environment')
self.experiment_definition = gdaserver.experiment_definition
self.metashop = gdaserver.metashop
self.meta = GDAMetadataProvider.getInstance()
#need to remove hardcoding
find("sample_thickness").asynchronousMoveTo(1.6)
self.progresscounter = 0
self.overheadsteps = 5
self.stepspersample = 8
if self.simulate:
print "running in simulation mode"
self.scannables = [self.detector, self.bsscscannable]
else:
self.cam = gda.factory.Finder.getInstance().find("bsaxscam")
self.scannables = [self.detector, self.bsscscannable, self.cam]
currentVisit = GDAMetadataProvider.getInstance().getMetadataValue("visit")
self.totalSteps = self.overheadsteps + self.bean.getMeasurements().size() * self.stepspersample
def getPosition(self):
'''If scan is running then pauses until status is okay and returning False
if the scan was not okay. If scan is not running, return the current state
and print a warning that the scan is not being paused.'''
self.statusRemainedGoodSinceLastGetPosition = 1.0
if JythonServerFacade.getInstance().getScanStatus() == RUNNING:
# loop until okay
while not self.getStatusAndReport():
# not okay
self.statusRemainedGoodSinceLastGetPosition = 0.0
sleep(self.secondsBetweenChecks)
# now okay
else: # scan not running
currentStatus = self.getStatus()
if not currentStatus: # bad
print "WaitBelowAndShutter not holding readback as no scan is running"
self.statusRemainedGoodSinceLastGetPosition = currentStatus
return self.statusRemainedGoodSinceLastGetPosition
def run(self):
# print "Thread: " + self.getName() + " started"
while (self.runThread):
if (JythonServerFacade.getInstance().getScanStatus()
== JythonStatus.RUNNING
and self.currenttemp >= float(MAXTEMP)):
JythonServerFacade.getInstance().pauseCurrentScan()
print "Scan paused as temperature " + self.getName(
) + " returns: " + str(self.currenttemp)
elif (JythonServerFacade.getInstance().getScanStatus()
== JythonStatus.PAUSED
and self.currenttemp <= float(MINTEMP)):
print "Scan resumed as temperature " + self.getName(
) + " returns: " + str(self.currenttemp)
JythonServerFacade.getInstance().resumeCurrentScan()
sleep(10)
def __init__(self, filename):
self.__version__ = '1.00'
self.hplcFile = filename
self.bean = HplcSessionBean.createFromXML(filename)
finder = gda.factory.Finder.getInstance()
find = finder.find
self.shutter = find('shutter')
self.bsdiode = find('bsdiode')
self.sample_type = find('sample_type')
self.sampleName = find("samplename")
self.environment = find("sample_environment")
self.tfg = finder.listAllLocalObjects("gda.device.Timer")[0]
self.ncddetectors = finder.listAllLocalObjects("uk.ac.gda.server.ncd.detectorsystem.NcdDetectorSystem")[0]
self.jsf = JythonServerFacade.getInstance()
self.readout_time = 0.1
#CREATE A LOGGER
self.logger = logging.getLogger('HPLC')
self.logger.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s: %(levelname)s: %(module)s: %(message)s',"[%Y-%m-%d %H:%M:%S]")
streamhandler = logging.StreamHandler()
streamhandler.setFormatter(formatter)
if len(self.logger.handlers) == 0:
self.logger.addHandler(streamhandler)
self.logger.info('HPLC class version '+self.__version__+' was instantiated')
def getPosition(self):
'''If scan is running then pauses until status is okay and returning False
if the scan was not okay. If scan is not running, return the current state
and print a warning that the scan is not being paused.
This only works if scan is not continuous.
'''
self.statusRemainedGoodSinceLastGetPosition = 1.0
if not self._operating_continuously:
if JythonServerFacade.getInstance().getScanStatus()==RUNNING:
# loop until okay
while not self._getStatusAndHandleChange():
# not okay
self.statusRemainedGoodSinceLastGetPosition = 0.0
sleep(self.secondsBetweenChecks)
self._collectNewMonitorValue()
# now okay
else: # scan not running
currentStatus = self._getStatus()
if not currentStatus: # bad
print self.name + " not holding read-back as no scan is running"
self.statusRemainedGoodSinceLastGetPosition = currentStatus
return self.statusRemainedGoodSinceLastGetPosition
will automatically be translated through this pre-processing step.
There are problems to this preprocessor approach. The main one is debugging.
All python sees is the pre-processed file, so if you have performed significant translation,
this may be very different from your source text.
Created on 16 Nov 2009
@author: fy65
'''
import tokenize
from gda.jython import JythonServerFacade
#from java.util import Vector
jsf=JythonServerFacade.getInstance()
gdaAlias = jsf.getAliasedCommands()
gdaAliasVararg = jsf.getAliasedVarargCommands().getAliasedCommands()
def translate(readline):
'''
translate GDA specific commands, i.e. alias, to true Jython syntax.
'''
firstInLoop = True
aliased = False
vararg_aliased = False
for type, name, _,_,_ in tokenize.generate_tokens(readline):
# convert to GDA commands to Jython functions
if type==tokenize.NAME:
if gdaAlias.contains(name):
def getLastScanPoint(self):
#jsf=InterfaceProvider.getJythonNamespace()
jsf = JythonServerFacade.getInstance()
lsdp = jsf.getLastScanDataPoint()
return lsdp
def __call__(self):
jsf = JythonServerFacade.getInstance()
for command in self.commands:
jsf.runCommand(command)
time.sleep(self.delay)
will automatically be translated through this pre-processing step.
There are problems to this preprocessor approach. The main one is debugging.
All python sees is the pre-processed file, so if you have performed significant translation,
this may be very different from your source text.
Created on 16 Nov 2009
@author: fy65
'''
import tokenize
from gda.jython import JythonServerFacade
#from java.util import Vector
jsf = JythonServerFacade.getInstance()
gdaAlias = jsf.getAliasedCommands()
gdaAliasVararg = jsf.getAliasedVarargCommands().getAliasedCommands()
def translate(readline):
'''
translate GDA specific commands, i.e. alias, to true Jython syntax.
'''
firstInLoop = True
aliased = False
vararg_aliased = False
for type, name, _, _, _ in tokenize.generate_tokens(readline):
# convert to GDA commands to Jython functions
if type == tokenize.NAME:
def go(self):
psc = self.makePathScan()
JythonServerFacade.getInstance().runCommand(psc)