def _getCurrentFileName(filenumber):
''' convert relative file number to its absolute path to the file with file extension as ".dat"'''
filename = str(filenumber)
if long(filenumber) < 0:
filename = os.path.join(PathConstructor.createFromDefaultProperty(),str(int(NumTracker(LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME)).getCurrentFileNumber()+int(filenumber)))+".dat")
else:
filename = os.path.join(PathConstructor.createFromDefaultProperty(),str(filenumber)+ ".dat")
return filename
def __init__(self, filespec=None, dir=None):
self.format = LocalProperties.get(
"gda.data.scan.datawriter.dataFormat")
if dir != None and dir != "None":
self.dir = dir
else:
self.dir = PathConstructor.createFromDefaultProperty()
self.beamline = GDAMetadataProvider.getInstance().getMetadataValue(
"instrument", LocalProperties.GDA_INSTRUMENT, "tmp")
if (self.format == "NexusDataWriter"):
#really should use scanFileName prefix rather than forcing to beamline-
self.prefix = LocalProperties.get("gda.data.filePrefix",
self.beamline + "-")
self.ext = "nxs"
if filespec == None:
filespec = "%d" % NumTracker(self.beamline).currentFileNumber
else:
self.prefix = ""
self.ext = "dat"
if filespec == None:
filespec = "%d" % NumTracker().currentFileNumber
filespec = filespec.__str__()
self.filename = self.tryFiles([
filespec, self.dir + "/" + filespec,
self.prefix + filespec + "." + self.ext,
self.dir + "/" + self.prefix + filespec + "." + self.ext,
self.dir + "/" + filespec + "." + self.ext
])
if (self.filename == None):
raise Exception("no file found for %s" % filespec)
def __init__(self, filespec=None, dir=None):
self.format = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
if dir!=None and dir != "None":
self.dir=dir
else:
self.dir = PathConstructor.createFromDefaultProperty()
self.beamline = GDAMetadataProvider.getInstance().getMetadataValue("instrument", LocalProperties.GDA_INSTRUMENT, "tmp")
if (self.format == "NexusDataWriter"):
#really should use scanFileName prefix rather than forcing to beamline-
self.prefix = LocalProperties.get("gda.data.filePrefix",self.beamline + "-")
self.ext = "nxs"
if filespec==None:
filespec = "%d" % NumTracker(self.beamline).currentFileNumber
else:
self.prefix = ""
self.ext = "dat"
if filespec==None:
filespec = "%d" % NumTracker().currentFileNumber
filespec = filespec.__str__()
self.filename = self.tryFiles([ filespec, self.dir+"/"+filespec, self.prefix+filespec+"."+self.ext, self.dir+"/"+self.prefix+filespec+"."+self.ext, self.dir+"/"+filespec+"."+self.ext ])
if (self.filename == None):
raise Exception("no file found for %s" % filespec)
def _getgdadir(self):
try:
import gda.data.PathConstructor as PathConstructor
datadir = PathConstructor.createFromDefaultProperty()
except ImportError:
print "No gda configuration access so please specify data directory"
raise
return datadir
def pescan(function=2, frequency=0.1, amplitude=10.0, shift=0.0, symmetry=50.0, number_of_pre_cycles=1,number_of_points_per_cycle=40.0, detector=mythen, ng=1, nf=1):
#setup function generator
fg.setFunction(function)
fg.setFrequency(frequency)
fg.setAmplitude(amplitude)
fg.setShift(shift)
fg.setSymmetry(symmetry)
sleep(2)
#derived parameters for pescan() function inputs
fg_frequency=fg.getFrequency()
fg_period=1/fg_frequency
starttime=number_of_pre_cycles * fg_period
stoptime=starttime+fg_period
gatewidth=fg_period/number_of_points_per_cycle
voltage.setNumberOfGates(ng)
electrometer.setNumberOfGates(ng)
voltage.addMonitor(1)
electrometer.addMonitor(1)
directory=PathConstructor.createFromDefaultProperty()
scanNumber=scanNumTracker.incrementNumber()
voltage.setFilename(directory+(str(scanNumber)))
electrometer.setFilename(directory+(str(scanNumber)))
#pre-conditioning
fg.setOutput(1)
timer=_Timer()
timer.start()
print "sample pre-conditioning cycles, please wait for %s" % starttime
while(not timer.hasElapsed(starttime)):
sleep(1)
#collection
collectionNumber=0
try:
for t1 in frange(starttime, stoptime, gatewidth):
#print t1
voltage.resetCounter()
voltage.setRepetition(collectionNumber)
electrometer.resetCounter()
electrometer.setRepetition(collectionNumber)
print "move event receiver to delay=%s width=%s" % (t1-starttime, gatewidth)
evr.moveTo([t1-starttime,gatewidth])
mythen.gated(nf, ng, scanNumber, collectionNumber)
collectionNumber += 1
#print "end loop"
interruptable()
except:
raise
finally:
print "end loop"
voltage.removeMonitor()
electrometer.removeMonitor()
#stop ramp output
fg.setOutput(0)
print "scan completed."
def pescan(self, frequency=0.1,exposure=0.5,amplitude=5.0,numPoints=40, func=2, bncycle=1):
self.directory=PathConstructor.createFromDefaultProperty()
self.scanNumber=scanNumTracker.incrementNumber()
self.filename=self.directory+(str(self.scanNumber))
print self.filename
if self.adc.getMode()=="Continuous":
self.setupADC2()
elif self.adc.getMode()=="Trigger":
self.configADC(200, self.adcClockRate(frequency))
self.calculateExperimentParameters(frequency, exposure, numPoints)
self.setupFG(freq=frequency,amp=amplitude,bncycle=self.numGates)
self.sampleConditioning(func=6, bncycle=1)
self.configTFG(frequency)
#self.setupDataCapturer()
print "open fast shutter %d" % time()
self.fastshutter.moveTo("OPEN")
if self.adc.getMode()=="Trigger":
print "enable adc sampling"
self.adc.enable()
try:
for i in range(self.numCycles):
GeneralCommands.pause()
#while not self.gateDetectorCompleted or not self.adcStreamerCompleted:
#if not self.gateDetectorCompleted:
# print "wait PSD to complete..."
#if not self.adcStreamerCompleted:
# print "wait ADC to finish PE data capture..."
#sleep(1.0)
self.startDetector(frequency, self.scanNumber, i)
#sleep(1.0)
if self.adc.getMode()=="Trigger":
print "enable adc sampling"
self.adc.enable()
elif self.adc.getMode()=="Continuous":
if frequency<=0.1:
self.startPEDataStreamer(self.filename+"_peg_"+str(i)+".h5", 1/frequency+TIME_FUDGE_FACTOR_IN_SECONDS)
else:
self.startPEDataStreamer(self.filename+"_peg_"+str(i)+".h5", 1/frequency*self.numGates*self.numFrames*self.numDefinedSequency+TIME_FUDGE_FACTOR_IN_SECONDS)
self.tfg.start()
if frequency<=0.1:
sleep(1/frequency+GDAPROCESSTIME)
else:
sleep(1/frequency*self.numGates*self.numFrames*self.numDefinedSequency+GDAPROCESSTIME*self.numDefinedSequency)
# while self.tfg.status() != "RUNNING":
# sleep(0.025)
# while self.tfg.status() != "IDLE":
# print self.tfg.progress()
# sleep(self.livetime)
#self.pedata.save(self.filename, i)
except:
raise
finally:
print "close fast shutter %d" % time()
self.fastshutter.moveTo("CLOSE")
print "collection completed at %d" % time()
self.stop()
def plots(startNumber, endNumber, commonSuffix="mythen_summed.dat", dataType=PSD):
firstPlot=True
datadir=PathConstructor.createFromDefaultProperty()
for filenumber in range(startNumber, endNumber+1):
filename=str(filenumber)+"-"+commonSuffix
if firstPlot:
plot(dataType, os.path.join(datadir,filename))
firstPlot=False
else:
plotover(dataType, os.path.join(datadir,filename))
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
# imagePath = PathConstructor.createFromProperty("gda.data.scan.datawriter.datadir");
imagePath=PathConstructor.createFromDefaultProperty() + File.separator;
fullPath = os.path.join(imagePath, subDir);
print "Note: Current Pilatus image path: " + fullPath;
self.imageProducer.setFilePath(fullPath);
self.imageProducer.setFilePrefix(newFilePrefix);
def pescan(func=2,freq=0.125,amp=5.0,shift=0.0,symmetry=50.0,trig=1,bmode=0,bncycle=1,bstate=1,
nprecycles=1,nptspercycle=40, det=mythen,
ng=1, nf=40):
#setup func generator 2
fg2.setFunction(func) # 2 - ramp
fg2.setAmplitude(amp)
fg2.setShift(shift)
fg2.setSymmetry(symmetry)
fg2.setTriggerSource(trig)
fg2.setBurstState(bstate) # switch on burst mode
fg2.setBurstMode(bmode)
fg2.setOutput(1)
fg2.setFrequency(freq)
fg2.setBurstNCycle(ng)
sleep(1)
#setup ADC to capture PE data
peobject.addMonitors()
peobject.setFirstData(True)
peobject.setNumberOfGates(ng)
#setup file name
directory=PathConstructor.createFromDefaultProperty()
scanNumber=scanNumTracker.incrementNumber()
peobject.setFilename(directory+(str(scanNumber)))
#collection
collectionNumber=1
numberToCollect=0
try:
peobject.reset() # reset the gate counter
print "open fast shutter %d" % time()
pos fastshutter "OPEN"
if freq <= 0.03:
print "GDA is ready for data collection, you need now to start TFG please. "
mythen.gated(nf, ng, scanNumber, collectionNumber) # block until all frames and gates are collected
else:
print "Please start PSD collection from QT window client"
sleep(5)
while (peobject.getCollectionNumber() <= nf):
if numberToCollect != peobject.getCollectionNumber():
numberToCollect=peobject.getCollectionNumber()
print "ready to collect frame %d, please wait..." % numberToCollect
pos fastshutter "CLOSE"
#peobject.save(collectionNumber)
collectionNumber += 1
except:
raise
finally:
print "collection completed at %d" % time()
peobject.removeMonitors() # ensure monitor removed
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
# imagePath = PathConstructor.createFromProperty("gda.data.scan.datawriter.datadir");
imagePath = PathConstructor.createFromDefaultProperty(
) + File.separator
fullPath = os.path.join(imagePath, subDir)
print "Note: Current Pilatus image path: " + fullPath
self.imageProducer.setFilePath(fullPath)
self.imageProducer.setFilePrefix(newFilePrefix)
def pescan(
starttime=pre_condition_time,
stoptime=stop_time,
gatewidth=gate_width,
mythen1=mythen,
ng=number_gates,
nf=number_frames,
):
# setup
voltage.setNumberOfGates(ng)
electrometer.setNumberOfGates(ng)
voltage.addMonitor(1)
electrometer.addMonitor(1)
directory = PathConstructor.createFromDefaultProperty()
scanNumber = scanNumTracker.incrementNumber()
voltage.setFilename(directory + ("/") + (str(scanNumber)))
electrometer.setFilename(directory + ("/") + (str(scanNumber)))
# pre-conditioning
fg.setOutput(1)
timer = _Timer()
timer.start()
print "sample pre-conditioning cycles, please wait for %s" % starttime
while not timer.hasElapsed(starttime):
sleep(1)
# collection
collectionNumber = 0
try:
for t1 in frange(starttime, stoptime, gatewidth):
# print t1
voltage.resetCounter()
voltage.setCollectionNumber(collectionNumber)
electrometer.resetCounter()
electrometer.setCollectionNumber(collectionNumber)
print "move event receiver to delay=%s width=%s" % (t1 - starttime, gatewidth)
evr.moveTo([t1 - starttime, gatewidth])
mythen.gated(nf, ng, scanNumber, mythen.getDataDirectory(), collectionNumber)
collectionNumber += 1
# print "end loop"
interruptable()
except:
raise
finally:
print "end loop"
voltage.removeMonitor()
electrometer.removeMonitor()
# clearup
# voltage.removeMonitor()
# electrometer.removeMonitor()
# stop ramp output
fg.setOutput(0)
print "scan completed."
def loadMythenRawData(filename):
'''load the mythen frame data.'''
from gda.device.detector.mythen.data import MythenRawDataset
if str(filename).startswith(File.separator):
try:
dataset = MythenRawDataset(java.io.File(filename))
except:
print "Fail to load data file: "+filename
return dataset
try:
dataset = MythenRawDataset(java.io.File(os.path.join(PathConstructor.createFromDefaultProperty(),str(filename))))
except:
print "Fail to load data file: "+filename
return dataset
def loadMythenData(filename):
'''load the mythen frame data.'''
from gda.device.detector.mythen.data import MythenProcessedDataset, MythenMergedDataset
if str(filename).startswith(File.separator):
try:
dataset = MythenProcessedDataset(java.io.File(filename))
except:
dataset = MythenMergedDataset(java.io.File(filename))
return dataset
if str(filename).find("merged") == -1:
if str(filename).find("summed") == -1:
#Not merged file or it is mythen data file
try:
dataset = MythenProcessedDataset(java.io.File(os.path.join(PathConstructor.createFromDefaultProperty(),str(filename))))
except:
dataset = MythenMergedDataset(java.io.File(os.path.join(PathConstructor.createFromDefaultProperty(),str(filename))))
else:
dataset = MythenMergedDataset(java.io.File(os.path.join(PathConstructor.createFromDefaultProperty(),str(filename))))
return dataset
else:
#externally merged file in 'processing' sub-folder
dataset = MythenMergedDataset(java.io.File(os.path.join(PathConstructor.createFromDefaultProperty(),str(filename))))
return dataset
def loadSRSData(filename):
'''Load SRS data file into a ScanFileHolder object,
supporting relative loading with respect to the current collected data (0)'''
sfh = ScanFileHolder()
try:
if filename == None:
#current file
sfh.load(SRSLoader(_getCurrentFileName(0)))
elif representsInt(filename):
#past file - relative path
sfh.load(SRSLoader(_getCurrentFileName(int(filename))))
elif not filename.startswith(File.separator):
#filename with extension
sfh.load(SRSLoader(os.path.join(PathConstructor.createFromDefaultProperty(),filename)))
else:
#absolute file path
sfh.load(SRSLoader(filename))
except ScanFileHolderException, err:
print "File loader failed. " + err
def loadMythenSRSFile(filename):
'''load MythenSRSFile, supporting relative file number with respect to the current one (0).'''
from gda.device.detector.mythen.data import MythenSrsFileLoader
filenamelist=[]
try:
if filename == None:
#current file
filenamelist=MythenSrsFileLoader().load(_getCurrentFileName(0))
elif representsInt(filename):
#past file - relative path
filenamelist=MythenSrsFileLoader().load(_getCurrentFileName(int(filename)))
elif not str(filename).startswith(File.separator):
#filename with extension
filenamelist=MythenSrsFileLoader().load(os.path.join(PathConstructor.createFromDefaultProperty(),filename))
else:
#absolute file path
filenamelist=MythenSrsFileLoader().load(filename)
except IOException, err:
print "MythenSrsFileLoader failed. " , err
def nwd():
dir = PathConstructor.createFromDefaultProperty()
filenumber = i11NumTracker.getCurrentFileNumber();
return os.path.join(dir, str(filenumber + 1))
def wd():
dir = PathConstructor.createFromDefaultProperty()
return dir
def atScanStart(self):
self.collectionNumber=0
self.directory=PathConstructor.createFromDefaultProperty()
self.scanNumber=scanNumTracker.getCurrentFileNumber()
self.filename=self.directory+(str(self.scanNumber))
def pescan(self, frequency=0.1,exposure=0.5,amplitude=5.0,numPoints=40, function=2, bncycle=1):
self.directory=PathConstructor.createFromDefaultProperty()
self.scanNumber=scanNumTracker.incrementNumber()
self.filename=self.directory+(str(self.scanNumber))
print self.filename
if self.adc.getMode()=="Gate":
self.setupADC2()
elif self.adc.getMode()=="Trigger":
self.configADC(200, self.adcClockRate(frequency))
self.calculateExperimentParameters(frequency, exposure, numPoints)
self.setupFG(freq=frequency,amp=amplitude,bncycle=self.numGates, func=function)
# must in following order
if self.isSampleConditioning():
self.sampleConditioning(func=6, bncycle=1)
self.configTFG(frequency)
self.setupDataCapturer(self.filename, self.numGates)
print "open fast shutter %d" % time()
self.fastshutter.moveTo("OPEN")
try:
if frequency <= self.boundaryFrequency:
for i in range(self.numCycles):
GeneralCommands.pause()
self.pedata.reset()
self.pedata.setCollectionNumber(i)
print "\ncollecting %d frames, %d gates per frame, Scan number %d, Collection number %d" % (self.numFrames*self.numDefinedSequency, self.numGates, self.scanNumber, i)
Thread(target=self.gateDetector, name="MythenGatedCollection", args=(self.numFrames, self.numGates, self.scanNumber, i), kwargs={}).start()
sleep(1)
#self.startDetector(frequency, self.scanNumber, i)
if self.adc.getMode()=="Trigger":
print "enable adc sampling"
self.adc.enable()
#elif self.adc.getMode()=="Continuous":
self.startPEDataStreamer(self.filename+"_pe_"+str(i)+".h5", 1/frequency+TIME_FUDGE_FACTOR_IN_SECONDS)
self.tfg.start()
sleep(1/frequency+GDAPROCESSTIME)
else:
finder=Finder.getInstance()
print "\nPlease start PSD collection from Mythen QT client ..."
print " 1. select 'Gated' option in the 'Runs' box first"
print " 2. then set 'Acquisition time' to %d, 'Repetitions' to %d" % (self.numGates, self.numFrames * self.numDefinedSequency*self.numCycles)
print " 3. set 'Output Directory' to subdirector %s under 'processing' directory, 'File name root' to %d, 'Start index' to %d" % (finder.find("GDAMetadata").getMetadataValue("subdirectory"), self.scanNumber, 0)
target = requestInput("Is PSD ready, Yes or No?")
print str(target)
if str(target)!="Yes":
raise "Exiting program"
for j in range(self.startCycleNumber,self.numCycles):
self.pedata.reset()
self.pedata.setCollectionNumber(j)
#self.startDetector(frequency, self.scanNumber, j)
for i in range(self.startSeqNumber, self.numDefinedSequency):
GeneralCommands.pause()
sleep(4.0)
self.tfg.config_cycle_for_seq(i, self.numGates, 1)
sleep(4.0)
if self.adc.getMode()=="Trigger":
print "enable adc sampling"
self.adc.enable()
#elif self.adc.getMode()=="Continuous":
self.startPEDataStreamer(self.filename+"_pe_"+str(i)+".h5", 1/frequency*self.numGates+TIME_FUDGE_FACTOR_IN_SECONDS)
self.tfg.start()
sleep(1/frequency*self.numGates+GDAPROCESSTIME)
except:
self.stop()
raise
finally:
print "close fast shutter %d" % time()
self.fastshutter.moveTo("CLOSE")
self.pedata.removeMonitors()
print "collection completed at %d" % time()
def datadir(self, *args):
if len(args) > 0:
raise ValueError(
"The data directory now depends on the visit. Use the 'visit' command to change this."
)
return PathConstructor.createFromDefaultProperty()
def pwd():
'''return the working directory'''
cwd = PathConstructor.createFromDefaultProperty()
return cwd
def nwf():
'''query the next working file path root'''
cwd = PathConstructor.createFromDefaultProperty()
filenumber = i11NumTracker.getCurrentFileNumber();
return os.path.join(cwd,str(filenumber+1))
def getVisitDirectory(self):
return PathConstructor.createFromDefaultProperty()
def pescan(func=2,freq=0.125,amp=5.0,shift=0.0,symmetry=50.0,trig=1,bmode=0,bncycle=1,bstate=0,
nprecycles=1,nptspercycle=40, det=mythen, ng=1, nf=1):
#setup func generator 2
fg2.setFunction(1) # square wave
fg2.setAmplitude(5.0)
fg2.setShift(2.5)
fg2.setDutyCycle(50.0)
fg2.setTriggerSource(trig)
fg2.setBurstState(0) # switch off burst mode before change burst parameters
if (freq<=0.125): # slow HV ramping
fg2.setFrequency(freq*nptspercycle)
fg2.setBurstNCycle(nptspercycle)
else: # fast HV ramping
fg2.setFrequency(freq)
fg2.setBurstNCycle(1)
fg2.setBurstMode(bmode)
fg2.setBurstState(1) #switch on burst mode
sleep(1)
#setup func generator 1
fg1.setFunction(func) # 2 - ramp
fg1.setFrequency(freq)
fg1.setAmplitude(amp)
fg1.setShift(shift)
fg1.setSymmetry(symmetry)
fg1.setTriggerSource(trig)
fg1.setBurstState(bstate) # switch off burst mode
fg1.setBurstMode(bmode)
fg1.setBurstNCycle(bncycle)
sleep(1)
#calculate acquisition parameters
fg1_frequency=fg1.getFrequency()
fg1_period=1/fg1_frequency
starttime=nprecycles * fg1_period
stoptime=starttime+fg1_period # only one cycle
gatewidth=fg1_period/nptspercycle # no need to minus file writing time as FIFO can buffer 4 frames
#setup ADC to capture PE data
peobject.addMonitor(1)
peobject.setFirstData(True)
#setup file name
directory=PathConstructor.createFromDefaultProperty()
scanNumber=scanNumTracker.incrementNumber()
peobject.setFilename(directory+(str(scanNumber)))
#pre-conditioning
evr.disable()
timer=_Timer()
timer.start()
fg2.setOutput(1)
fg1.setOutput(1)
print "sample pre-conditioning cycles, please wait for %s" % starttime
while(not timer.hasElapsed(starttime)):
sleep(0.01)
#collection
collectionNumber=0
evr.enableField()
try:
if (freq<=0.125): # 8sec period, 200ms per point
peobject.reset()
peobject.setFastMode(False)
evr.moveTo([0.0,gatewidth-0.15]) #150 ms writing to disk allowed
print "move event receiver to delay=%s width=%s" % (evr.getDelay(), evr.getWidth())
print "start mythen %d" % time()
pos fastshutter "OPEN"
mythen.gated(nptspercycle, ng, scanNumber)
pos fastshutter "CLOSE"
peobject.save()
else:
peobject.setFastMode(True)
for t1 in frange(starttime, stoptime, gatewidth)[:-1]:
#print t1
peobject.reset() # reset the gate counter
print "move event receiver to delay=%s width=%s" % (t1-starttime, gatewidth)
evr.moveTo([t1-starttime,gatewidth])
print "start mythen %d" % time()
pos fastshutter "OPEN"
mythen.gated(nf, ng, scanNumber, collectionNumber) # block until all frames and gates are collected
pos fastshutter "CLOSE"
collectionNumber += 1
peobject.save(collectionNumber)
interruptable() # allow "StopAll" to work
except:
raise
finally:
print "collection completed at %d" % time()
peobject.removeMonitor() # ensure monitor removed
pestop()
#stop ramp output
fg2.setOutput(0)
fg1.setOutput(0)
def lwf():
'''return the last working file path root'''
cwd = PathConstructor.createFromDefaultProperty()
filenumber = i11JNumTracker.getCurrentFileNumber();
return os.path.join(cwd,str(filenumber))
def datadir(self, *args):
if len(args) > 0:
raise ValueError("The data directory now depends on the visit. Use the 'visit' command to change this.")
return PathConstructor.createFromDefaultProperty()
def getVisitDirectory(self):
return PathConstructor.createFromDefaultProperty()