def analyserpathscan_v1(scannables, path, *args):
'''
perform a single region analyser data collection at each point on the specified path,
and produce a single scan data files recording scannables' poistions and metadata, and
analyser data for the active region defined in your sequence definition file under ew4001 node.
implementation details:
This function pre-process sequence file to set up Region Position Provider for scannable
'regions' ready for data collection using analyser 'ew4001', then delegate the scan
process to 'pathscan'.
'''
newargs = []
i = 0
while i < len(args):
arg = args[i]
newargs.append(arg)
i = i + 1
if isinstance(arg, RegionScannable):
controller = Finder.find("SequenceFileObserver")
xmldir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + "xml" + os.sep
filename = xmldir + args[i]
if (OsUtil.isWindows()):
FilenameUtil.setPrefix("D:")
filename = FilenameUtil.convertSeparator(filename)
controller.update(controller, SequenceFileChangeEvent(filename))
sleep(1.0)
while (InterfaceProvider.getScanStatusHolder().getScanStatus() ==
JythonStatus.PAUSED):
sleep(1.0)
newargs.append(RegionPositionProvider(filename))
#newargs.append( arg ) # to read the actual position
i = i + 1
pathscan(scannables, path, newargs)
def analyserscan_v1(*args):
starttime = time.ctime()
if PRINTTIME: print "=== Scan started: " + starttime
newargs = []
i = 0
while i < len(args):
arg = args[i]
newargs.append(arg)
i = i + 1
if isinstance(arg, RegionScannable):
controller = Finder.find("SequenceFileObserver")
xmldir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + "xml" + os.sep
filename = xmldir + args[i]
if (OsUtil.isWindows()):
FilenameUtil.setPrefix("D:")
filename = FilenameUtil.convertSeparator(filename)
controller.update(controller, SequenceFileChangeEvent(filename))
sleep(1.0)
while (InterfaceProvider.getScanStatusHolder().getScanStatus() ==
JythonStatus.PAUSED):
sleep(1.0)
newargs.append(RegionPositionProvider(filename))
#newargs.append( arg ) # to read the actual position
i = i + 1
scan(newargs)
if PRINTTIME:
print("=== Scan ended: " + time.ctime() +
". Elapsed time: %.0f seconds" % (time.time() - starttime))
def cwd(subdir=None):
if subdir==None:
metadata.setMetadataValue("subdirectory","")
else:
sane=re.compile("[^a-zA-Z0-9-_:]")
subdir=sane.sub("",subdir)
metadata.setMetadataValue("subdirectory",subdir)
print InterfaceProvider.getPathConstructor().createFromDefaultProperty()
def zacstop():
try:
fastEnergy.stop()
beamlineutil.restoreArchiving()
InterfaceProvider.getCommandAborter().abortCommands()
except:
errortype, exception, traceback = sys.exc_info()
logger.fullLog(None, "Error in stopping the zacscan ", errortype,
exception, traceback, False)
def setUp(self):
InterfaceProvider.setTerminalPrinterForTesting(
MockJythonServerFacade())
self.abspath = os.path.abspath(TestFileFolder + "/1.nxs")
parentPath = os.path.split(self.abspath)[0]
if not os.path.isdir(parentPath):
os.makedirs(parentPath)
if os.path.isfile(self.abspath):
os.remove(self.abspath)
def configureFileWriterPlugin(self, areadet,numImages):
if not isinstance(areadet, NXDetector):
raise Exception("'%s' detector is not a NXDetector! " % (areadet.getName()))
additional_plugin_list = areadet.getAdditionalPluginList()
datawriter=None
scanNumber=nfn()
for each in additional_plugin_list:
if isinstance(each, MultipleImagesPerHDF5FileWriter):
datawriter=each
datawriter.getNdFile().getPluginBase().disableCallbacks()
datawriter.getNdFile().getPluginBase().setBlockingCallbacks(0)
filePathUsed = InterfaceProvider.getPathConstructor().createFromDefaultProperty() + "/"
f=File(filePathUsed)
if not f.exists():
if not f.mkdirs():
raise Exception("Folder does not exist and cannot be made: " + str(filePathUsed))
datawriter.getNdFile().setFilePath(filePathUsed)
if not datawriter.getNdFile().filePathExists():
raise Exception("Path does not exist on IOC '" + filePathUsed + "'")
datawriter.getNdFile().setFileName("pco")
datawriter.getNdFile().setFileNumber(scanNumber)
datawriter.getNdFile().setAutoIncrement(0)
datawriter.getNdFile().setAutoSave(0)
datawriter.getNdFile().setFileWriteMode(2);
datawriter.getNdFileHDF5().setStoreAttr(0)
datawriter.getNdFileHDF5().setStorePerform(0)
datawriter.getNdFileHDF5().setLazyOpen(True);
datawriter.getNdFileHDF5().setBoundaryAlign(0);
datawriter.getNdFileHDF5().setNumCapture(numImages);
datawriter.getNdFileHDF5().setNumRowChunks(0);
datawriter.getNdFileHDF5().setNumColChunks(0);
datawriter.getNdFileHDF5().setNumFramesChunks(0);
datawriter.getNdFileHDF5().setNumFramesFlush(0);
datawriter.getNdFileHDF5().startCapture();
datawriter.getNdFile().getPluginBase().enableCallbacks()
elif isinstance(each, SingleImagePerFileWriter):
datawriter=each
datawriter.getNdFile().getPluginBase().disableCallbacks()
filePathUsed = InterfaceProvider.getPathConstructor().createFromDefaultProperty() + "/" + str(scanNumber) + "_PCOImage/"
f=File(filePathUsed)
if not f.exists():
if not f.mkdirs():
raise Exception("Folder does not exist and cannot be made: " + str(filePathUsed))
datawriter.getNdFile().setFilePath(filePathUsed)
if not datawriter.getNdFile().filePathExists():
raise Exception("Path does not exist on IOC '" + filePathUsed + "'")
datawriter.getNdFile().setFileName("pco")
datawriter.getNdFile().setFileNumber(1)
datawriter.getNdFile().setAutoIncrement(1)
datawriter.getNdFile().setAutoSave(1)
datawriter.getNdFile().setFileWriteMode(0)
datawriter.getNdFile().getPluginBase().enableCallbacks()
if datawriter is None:
raise Exception("Cannot find EPICS File Writer Plugin for detector %s" % (areadet.getName()))
def analyserpathscan(*args):
'''
perform single/multiple regions analyser data collection at each point on the specified path,
and produce a single scan file recording all scannables' poistions and metadata, along with
analyser scan data under region's name as NXdetector node.
implementation details:
This function pre-process sequence file to set up analyser 'ew4000' ready for data collection.
It creates scannable group to support point-to-point concurrent scan.
'''
starttime = time.ctime()
if PRINTTIME: print "=== Scan started: " + starttime
newargs = []
i = 0
while i < len(args):
arg = args[i]
if type(arg) == TupleType:
if allElementsAreScannable(arg):
scannableGroup = ScannableGroup("pathgroup")
for each in arg:
scannableGroup.addGroupMember(each)
newargs.append(scannableGroup)
elif allElementsAreListOfNumber(arg):
newargs.append(arg)
else:
raise TypeError, "Only tuple of scannables and tuple of list of numbers are supported."
else:
newargs.append(arg)
i = i + 1
if isinstance(arg, EW4000):
controller = Finder.find("SequenceFileObserver")
xmldir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + "xml" + os.sep
filename = xmldir + args[i]
if (OsUtil.isWindows()):
FilenameUtil.setPrefix("D:")
filename = FilenameUtil.convertSeparator(filename)
controller.update(controller, SequenceFileChangeEvent(filename))
sleep(2.0)
jythonServerStatus = InterfaceProvider.getJythonServerStatusProvider(
).getJythonServerStatus()
while (jythonServerStatus.isScriptOrScanPaused()):
sleep(1.0)
arg.setSequenceFilename(filename)
sequence = arg.loadSequenceData(filename)
if isinstance(arg.getCollectionStrategy(),
EW4000CollectionStrategy):
arg.getCollectionStrategy().setSequence(sequence)
i = i + 1
scan(newargs)
if PRINTTIME:
print("=== Scan ended: " + time.ctime() +
". Elapsed time: %.0f seconds" % (time.time() - starttime))
def fullLog(self, controller, msg, exceptionType=None, exception=None, traceback=None, Raise=False): msg = self.createMessage(msg, exceptionType, exception, traceback); if controller != None: controller.update(None, msg); if exception != None: self.logger.error(msg); else: self.logger.info(msg); InterfaceProvider.getTerminalPrinter().print(msg); if Raise: if isinstance(msg, Exception): raise msg; raise Exception(msg);
def log(controller, msg, exceptionType=None, exception=None, traceback=None, Raise=False, logger=logger):
msg = str(msg)
msg = constructMessage(msg, exceptionType, exception, None)
if controller:
controller.update(None, msg);
if logger:
if exception:
logger.error(constructMessage(msg, exceptionType, exception, traceback))
else:
logger.info(msg)
InterfaceProvider.getTerminalPrinter().print(msg)
if Raise:
if isinstance(msg, Exception):
raise msg
raise Exception(msg)
def createPVScannable( name, pv, addToNameSpace=True, hasUnits=True, getAsString=False):
"""
utility function to create a scannable from a PV
arguments:
name - of scannable
pv - pv
addToNameSpace = if True the scannable is accessible from the commandline after the call
hasUnits - default True. The value is a number and support is given for setUserUnits
getAsString - default False. Useful if the PV is an enum as it returns the string representation.
If true also set hasUnits to False
e.g.
createPVScannable("acoll_average_size", "BL13J-OP-ACOLL-01:AVERAGESIZE", True)
"""
sc = EpicsScannable()
sc.setName(name)
sc.setPvName(pv)
sc.setUseNameAsInputName(True)
sc.setHasUnits(hasUnits)
sc.setGetAsString(getAsString)
sc.afterPropertiesSet()
sc.configure()
if addToNameSpace:
commandServer = InterfaceProvider.getJythonNamespace()
commandServer.placeInJythonNamespace(name,sc)
return sc
def doCalibration(self, calibrant='Si', calibrant_x=0, calibrant_y=0, calibrant_exposure=1.0):
if self.calibration_required:
mycalibrant=Finder.getInstance().find("calibrant_name")
mycalibrant.moveTo(calibrant)
dummyScannable=DummyScannable("dummyScannable")
#additional_plugin_list = pixium.getAdditionalPluginList()[0]
#Detector calibration
if self.calibration_required:
self.stage_x.moveTo(calibrant_x)
self.stage_y.moveTo(calibrant_y)
scan([dummyScannable, 1, 1, 1, self.pixium, calibrant_exposure])
#TODO GDA .nxs file, not EPICS h5 file
scan_data_point_provider = InterfaceProvider.getScanDataPointProvider()
self.calibrant_file_name = scan_data_point_provider.getLastScanDataPoint().getCurrentFilename()
#calibrant_file_name = additional_plugin_list.getFullFileName()
#do detector calibration on cluster serevrs
builder = OSCommandRunnerBuilder.defaults()
builder=builder.command([LocalProperties.get("org.opengda.lde.pixium.data.reduction.script","/dls_sw/apps/i11-scripts/bin/LDE-RunFromGDAAtEndOfScan.sh")])
builder=builder.keepOutput(True)
builder = builder.inputFilename(self.calibrant_file_name)
builder = builder.outputFilename(os.path.splitext(self.calibrant_file_name)[0]+"_output.log")
builder=builder.noTimeout()
builder.build()
self.calibration_required=False
def lastscan(extension="tmp"):
nt = NumTracker(extension)
lastSRSFileName = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + File.separator + str(
nt.getCurrentFileNumber()) + ".dat"
del nt
return lastSRSFileName
def setFile(self, subDir=None, newFilePrefix=None):
"""Set file path and name"""
if subDir is not None:
self.subDir = str(subDir)
if newFilePrefix is not None:
self.filePrefix = str(newFilePrefix)
pilatusDataDir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()
fullPath = os.path.join(pilatusDataDir, self.subDir)
if not os.path.exists(fullPath):
print "Warning: Pilatus image path does not exist. Create new"
print "OS Command: " + "umask 0002; mkdir -p " + fullPath
os.system("umask 0002; mkdir -p " + fullPath)
# Check the new path created.
if not os.path.exists(fullPath):
print "Error: Pilatus image path does not exist and can not be created"
return
print "Note: Current Pilatus image path: " + fullPath
self.detector.getNdFile().setFilePath(fullPath)
self.detector.getNdFile().setFileName(self.filePrefix)
def createPVScannable(name,
pv,
addToNameSpace=True,
hasUnits=True,
getAsString=False):
"""
utility function to create a scannable from a PV
arguments:
name - of scannable
pv - pv
addToNameSpace = if True the scannable is accessible from the commandline after the call
hasUnits - default True. The value is a number and support is given for setUserUnits
getAsString - default False. Useful if the PV is an enum as it returns the string representation.
If true also set hasUnits to False
e.g.
createPVScannable("acoll_average_size", "BL13J-OP-ACOLL-01:AVERAGESIZE", True)
"""
sc = EpicsScannable()
sc.setName(name)
sc.setPvName(pv)
sc.setUseNameAsInputName(True)
sc.setHasUnits(hasUnits)
sc.setGetAsString(getAsString)
sc.afterPropertiesSet()
sc.configure()
if addToNameSpace:
commandServer = InterfaceProvider.getJythonNamespace()
commandServer.placeInJythonNamespace(name, sc)
return sc
def setTerminalLogger(self, newLoggerName="gda_terminal.log"):
tlPath = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()
tlFile = os.path.join(tlPath, newLoggerName)
tlpp = Finder.find("terminallog_path_provider")
tlpp.setTemplate(str(tlFile))
def saveSRSData(self, energy, pol, fileList):
srsHeader=[" &SRS\n", " SRSRUN=null,SRSDAT=null,SRSTIM=null,\n", " SRSSTN='null',SRSPRJ='null ',SRSEXP='null ',\n", " SRSTLE=' ',\n", " SRSCN1=' ',SRSCN2=' ',SRSCN3=' ',\n", " &END\n"];
try:
runs=NumTracker("tmp")
currentNum = runs.getCurrentFileNumber()
#currentNum = runs.incrementNumber()
path = InterfaceProvider.getPathConstructor().createFromProperty("gda.data.scan.datawriter.datadir")
fileName = path + "/" + str(currentNum) + ".dat"
# print fileName
fh=open(fileName, 'w');
#SRS Header
for i in range(len(srsHeader)):
fh.write(srsHeader[i]);
titleLine='%(v1)s \t %(v2)s \t %(v3)s \n' %{'v1': self.energyDevice.getName(), 'v2': self.polarisationDevice.getName(), 'v3': self.detector.getName()};
fh.write(titleLine);
nf=len(fileList);
for n in range(nf):
#print i, arrayEnergyPGM[i], arrayEnergyIDGAP[i], arrayChannel01[i], arrayChannel02[i], arrayChannel03[i], arrayChannel04[i];
newLine='%(v1).8f \t %(v2)s \t %(v3)s \n' %{'v1': energy[n], 'v2': pol[n], 'v3': fileList[n]};
fh.write(newLine);
fh.close();
print "Scan complete. File saved in " + fileName;
except:
print "ERROR: Could not save data into file."
def setNewImagePath(self):
"""Set file path and name based on current scan run number"""
next_num = NumTracker("tmp").getCurrentFileNumber()
base_path = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + File.separator
sub_dir = "%d_%s" % (next_num, self.pathPostfix)
new_image_path = os.path.join(base_path, sub_dir)
if not os.path.exists(new_image_path):
#print("Path does not exist. Create new one.")
os.makedirs(new_image_path)
self.resetImageNumber()
if not os.path.isdir(new_image_path):
print("Invalid path")
return
self.filePath = new_image_path
#print("Image file path set to " + self.filePath)
nd_file = self.detector.getNdFile()
nd_file.setFilePath(self.filePath)
nd_file.setFileName(self.filePrefix)
nd_file.setFileTemplate(self.fileFormat)
nd_file.setAutoIncrement(True)
nd_file.setAutoSave(True)
nd_file.setFileFormat(0)
#Magic file format depending on the file extension
return self.filePath
def saveSRSData(self, numberOfPoints):
srsHeader = [
" &SRS\n", " SRSRUN=null,SRSDAT=null,SRSTIM=null,\n",
" SRSSTN='null',SRSPRJ='null ',SRSEXP='null ',\n",
" SRSTLE=' ',\n",
" SRSCN1=' ',SRSCN2=' ',SRSCN3=' ',\n",
" &END\n"
]
try:
runs = NumTracker("tmp")
nextNum = runs.getCurrentFileNumber()
#nextNum = runs.incrementNumber()
path = InterfaceProvider.getPathConstructor().createFromProperty(
"gda.data.scan.datawriter.datadir")
fileName = path + "/" + str(nextNum + 1) + ".dat"
print fileName
fh = open(fileName, 'w')
#SRS Header
for i in range(len(srsHeader)):
fh.write(srsHeader[i])
titleLine = '%(v1)s \t %(v2)s \t %(v3)s \t %(v4)s \t %(v5)s \t %(v6)s \n' % {
'v1': 'PGM Energy',
'v2': 'ID GAP Energy',
'v3': 'Channel 1',
'v4': 'Channel 2',
'v5': 'Channel 3',
'v6': 'Channel 4'
}
fh.write(titleLine)
arrayEnergyPGM = self.energyPGM.cagetArrayDouble()
arrayEnergyIDGAP = self.energyIDGAP.cagetArrayDouble()
arrayChannel01 = self.channel01.cagetArrayDouble()
arrayChannel02 = self.channel02.cagetArrayDouble()
arrayChannel03 = self.channel03.cagetArrayDouble()
arrayChannel04 = self.channel04.cagetArrayDouble()
for i in range(numberOfPoints):
if arrayEnergyPGM[i] < self.se:
continue
if arrayEnergyPGM[i] > self.ee:
continue
#print i, arrayEnergyPGM[i], arrayEnergyIDGAP[i], arrayChannel01[i], arrayChannel02[i], arrayChannel03[i], arrayChannel04[i];
newLine = '%(v1).8f \t %(v2).8f \t %(v3).8f \t %(v4).8f \t %(v5).8f \t %(v6).8f \n' % {
'v1': arrayEnergyPGM[i],
'v2': arrayEnergyIDGAP[i],
'v3': arrayChannel01[i],
'v4': arrayChannel02[i],
'v5': arrayChannel03[i],
'v6': arrayChannel04[i]
}
fh.write(newLine)
fh.close()
runs.incrementNumber()
except:
print "ERROR: Could not save data into file."
def checkPath(self):
# self.subDir=str(subDir);
# self.filePrefix = str(newFilePrefix);
imagePath = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()
fullPath = os.path.join(imagePath, self.subDir)
if fullPath != self.getFilePath():
self.setFile()
return
def writeDataToFile(self, data=[]):
filenumber = NumTracker("i10").getCurrentFileNumber();
waveformfilename=str(InterfaceProvider.getPathConstructor().createFromDefaultProperty())+"/"+ str("i10-")+str(filenumber)+"-"+str(self.getName())+"_"+str(self.pointNumber)+".dat"
print waveformfilename
datafile=open(waveformfilename, 'w')
for value in data:
datafile.write(str(value)+'\n')
datafile.flush()
datafile.close()
return waveformfilename
def analyserpathscan(scannables, path, *args):
'''
perform single/multiple regions analyser data collection at each point on the specified path,
and produce a single scan file recording all scannables' poistions and metadata, along with
analyser scann data under region's name as NXdetector node.
implementation details:
This function pre-process sequence file to set up analyser 'ew4000' ready for data collection,
then delegate the scan process to 'pathscan'.
'''
starttime = time.ctime()
if PRINTTIME: print "=== Scan started: " + starttime
newargs = []
i = 0
while i < len(args):
arg = args[i]
newargs.append(arg)
i = i + 1
if isinstance(arg, EW4000):
controller = Finder.find("SequenceFileObserver")
xmldir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + "xml" + os.sep
filename = xmldir + args[i]
if (OsUtil.isWindows()):
FilenameUtil.setPrefix("D:")
filename = FilenameUtil.convertSeparator(filename)
controller.update(controller, SequenceFileChangeEvent(filename))
sleep(2.0)
jythonServerStatus = InterfaceProvider.getJythonServerStatusProvider(
).getJythonServerStatus()
while (jythonServerStatus.isScriptOrScanPaused()):
sleep(1.0)
arg.setSequenceFilename(filename)
sequence = arg.loadSequenceData(filename)
if isinstance(arg.getCollectionStrategy(),
EW4000CollectionStrategy):
arg.getCollectionStrategy().setSequence(sequence)
i = i + 1
pathscan(scannables, path, newargs)
if PRINTTIME:
print("=== Scan ended: " + time.ctime() +
". Elapsed time: %.0f seconds" % (time.time() - starttime))
def getSrsFileName(scanNumber=None):
if scanNumber is None:
sn = getScanNumber()
else:
sn = scanNumber
srsPath = InterfaceProvider.getPathConstructor().createFromProperty(
"gda.data.scan.datawriter.datadir")
srsFileName = srsPath + File.separator + str(sn) + ".dat"
print "srs file name is: " + srsFileName
return srsFileName
def _write_saveinfo_file(self):
if DEBUG:
print "writing saveinfo file for directory:", self._get_target_directory(
)
saveinfofilepath = os.path.join(PARAMETER_FILES_PATH, "saveinfo.txt")
saveinfofile = open(saveinfofilepath, mode='w')
paths = "Z:" + InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()[10:]
savepath = os.path.join(paths,
"%05i-%s-files" % (self.scannumber, self.name))
saveinfofile.write(savepath + "/\r\n%05d" % self._next_image_number)
saveinfofile.close()
def incrementFilename(self):
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
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.interrupted = Boolean(0)
def log(controller,
msg,
exceptionType=None,
exception=None,
traceback=None,
Raise=False,
logger=logger):
msg = str(msg)
msg = constructMessage(msg, exceptionType, exception, None)
if controller:
controller.update(None, msg)
if logger:
if exception:
logger.error(
constructMessage(msg, exceptionType, exception, traceback))
else:
logger.info(msg)
InterfaceProvider.getTerminalPrinter().print(msg)
if Raise:
if isinstance(msg, Exception):
raise msg
raise Exception(msg)
def getDir(proposal=None, visit=1):
if proposal is None: # the default commissioning proposal
userDir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty() + File.separator
print "Current User Data Directory: " + userDir
else:
# get current Year
currentTime = localtime()
currentYear = currentTime[0]
userDir = +proposal + "-" + str(visit)
userDir = "/dls/" + beamlineName + "/data/" + str(
currentYear) + "/" + proposal + "-" + str(visit)
print userDir + " should the user data directory for this proposal and visit."
def prepareForCollection(self):
self._next_image_number = 1
self.scannumber = InterfaceProvider.getCurrentScanInformationHolder(
).getCurrentScanInformation().getScanNumber()
# Create folder for scannumber '12345-' + name + '-files'
self._write_commands_file(self.getCollectionTime())
self._write_background_file(self.background)
self._write_saveinfo_file()
target_dir = self._get_target_directory()
if not os.path.exists(target_dir):
os.makedirs(target_dir)
time.sleep(5)
def exportFinalBeans(self):
"""The samples are updated to include the datafile paths
export readonly version of .biosaxs file to keep record of experiment"""
fname = self.beanFile.split(os.path.sep)[-1].rsplit('.', 1)[0]
now = datetime.datetime.now().strftime('_%Y%m%d_%H%M%S')
user_visit = InterfaceProvider.getBatonStateProvider().getBatonHolder().getVisitID()
prop = PathConstructor.getDefaultPropertyName()
path = PathConstructor.createFromProperty(prop, HashMap({'visit': user_visit}))
full_path = os.path.join(path, fname + now + '.biosaxs')
BSSCSessionBean.writeToXML(self.bean, full_path)
os.chmod(full_path, 0444)
def getSrsFileName(self, scanNumber=None, srsPath=None):
if scanNumber is None:
nt = NumTracker("tmp")
sn = nt.getCurrentFileNumber()
else:
sn = scanNumber
if srsPath is None:
srsPath = InterfaceProvider.getPathConstructor(
).createFromProperty("gda.data.scan.datawriter.datadir")
srsFileName = srsPath + File.separator + str(sn) + ".dat"
# print "srs file name is: " + srsFileName;
return srsFileName
def exportFinalBeans(self):
"""The samples are updated to include the datafile paths
export readonly version of .biosaxs file to keep record of experiment"""
fname = self.beanFile.split(os.path.sep)[-1].rsplit('.', 1)[0]
now = datetime.datetime.now().strftime('_%Y%m%d_%H%M%S')
user_visit = InterfaceProvider.getBatonStateProvider().getBatonHolder(
).getVisitID()
prop = PathConstructor.getDefaultPropertyName()
path = PathConstructor.createFromProperty(
prop, HashMap({'visit': user_visit}))
full_path = os.path.join(path, fname + now + '.biosaxs')
BSSCSessionBean.writeToXML(self.bean, full_path)
os.chmod(full_path, 0444)
def setFile(self, subDir=None, newFilePrefix=None):
"""Set file path and name"""
if subDir is not None:
self.subDir = str(subDir)
if newFilePrefix is not None:
self.filePrefix = str(newFilePrefix)
# imagePath = InterfaceProvider.getPathConstructor().createFromProperty("gda.data.scan.datawriter.datadir");
# imagePath=InterfaceProvider.getPathConstructor().createFromDefaultProperty() + File.separator;
imagePath = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()
fullPath = os.path.join(imagePath, self.subDir)
print "Image path for %s is set to %s." % (self.getName(), fullPath)
self.imageProducer.setFilePath(fullPath)
self.imageProducer.setFilePrefix(self.filePrefix)
def ls_pv_scannables(PV=""):
"""
Function to list Scannables associated with EPICs PVs, the PV and the associated DESC field
Usage:
>ls_pv_scannables()
or
>ls_pv_scannables(<PV>)
"""
from gda.device.scannable import ScannableMotor
from gda.device.motor import EpicsMotor
scannableConnectedToPV = None
a = InterfaceProvider.getJythonNamespace().getNamesForAllObjectsOfType(
Findable)
l = filter(
lambda x: isinstance(x, EpicsScannable) or
(isinstance(x, ScannableMotor) and isinstance(x.motor, EpicsMotor)),
a.values().toArray())
for x in l:
description = "unknown"
pvName = "unknown"
if isinstance(x, EpicsScannable):
pvName = x.pvName
if isinstance(x, ScannableMotor) and isinstance(x.motor, EpicsMotor):
pvName = x.motor.pvName
if PV != "":
if PV.upper() == pvName.upper():
scannableConnectedToPV = x
break
else:
if x.configured:
try:
description = caget(pvName + ".DESC")
except:
description = "Unable to read description"
pass
else:
description = "Not configured!"
print x.name, pvName, description
if PV != "":
if scannableConnectedToPV is None:
print "No scannable found for PV " + PV
print "Scannable " + x.name + " is connected to ", PV
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
# imagePath = InterfaceProvider.getPathConstructor().createFromProperty("gda.data.scan.datawriter.datadir");
imagePath=InterfaceProvider.getPathConstructor().createFromDefaultProperty() + File.separator;
newFilePath = os.path.join(imagePath, subDir);
if not os.path.exists(newFilePath):
print "Path does not exist. Create new one."
os.makedirs(newFilePath);
if not os.path.isdir(newFilePath):
print "Invalid path";
return;
self.filePath = newFilePath;
self.filePrefix = newFilePrefix
print "Image file path set to " + self.filePath;
def createScannableFromPV( name, pv, addToNameSpace=True, getAsString=True, hasUnits=False):
"""
Description:
utility function to create a scannable from a given PV
Arguments:
name - user-specified name of a scannable to be created, e.g. pixium10_DataType
pv - EPICS identifier of pv to be used by the scannable, e.g. BL12I-EA-DET-10:CAM:DataType
addToNameSpace = if True, the scannable is accessible from the commandline after the call
getAsString - If True, output value is a string (useful for enum pv, in which case set getAsString=True, and set hasUnits=False)
hasUnits - If False, output value is not converted to units - useful for enum pv with getAsString=True
For example,
createScannableFromPV("pixium10_DataType", "BL12I-EA-DET-10:CAM:DataType", True, True, False)
creates a scannable for pv with the following enums:
caget -d 31 BL12I-EA-DET-10:CAM:DataType
BL12I-EA-DET-10:CAM:DataType
Native data type: DBF_ENUM
Request type: DBR_CTRL_ENUM
Element count: 1
Value: UInt32
Status: NO_ALARM
Severity: NO_ALARM
Enums: ( 8)
[ 0] Int8
[ 1] UInt8
[ 2] Int16
[ 3] UInt16
[ 4] Int32
[ 5] UInt32
[ 6] Float32
[ 7] Float64
"""
sc = EpicsScannable()
sc.setName(name)
sc.setPvName(pv)
sc.setUseNameAsInputName(True)
sc.setGetAsString(getAsString)
sc.setHasUnits(hasUnits)
sc.afterPropertiesSet()
sc.configure()
if addToNameSpace:
commandServer = InterfaceProvider.getJythonNamespace()
commandServer.placeInJythonNamespace(name,sc)
return sc
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 ls_pv_scannables( PV=""):
"""
Function to list Scannables associated with EPICs PVs, the PV and the associated DESC field
Usage:
>ls_pv_scannables()
or
>ls_pv_scannables(<PV>)
"""
from gda.device.scannable import ScannableMotor
from gda.device.motor import EpicsMotor
scannableConnectedToPV=None
a=InterfaceProvider.getJythonNamespace().getAllFromJythonNamespace()
l=filter(lambda x: isinstance(x, EpicsScannable) or (isinstance(x, ScannableMotor) and isinstance(x.motor, EpicsMotor)), a.values().toArray())
for x in l:
description="unknown"
pvName ="unknown"
if isinstance(x, EpicsScannable):
pvName=x.pvName
if isinstance(x, ScannableMotor) and isinstance(x.motor, EpicsMotor):
pvName=x.motor.pvName
if PV != "":
if PV.upper() == pvName.upper():
scannableConnectedToPV=x
break
else:
if x.configured:
try:
description = caget(pvName + ".DESC")
except:
description = "Unable to read description"
pass
else:
description = "Not configured!"
print x.name, pvName, description
if PV != "":
if scannableConnectedToPV is None:
print "No scannable found for PV " + PV
print "Scannable " + x.name + " is connected to ", PV
def doSampleDataCollection(self, sample_x_start=None, sample_x_stop=None, sample_x_step=None, sample_y_start=None, sample_y_stop=None, sample_y_step=None, sample_exposure=1.0):
# sample diffraction data
args=[]
if sample_x_start is not None or sample_x_stop is not None or sample_x_step is not None:
args.append(self.stage_x)
if sample_y_start is not None:
args.append(sample_x_start)
if sample_y_stop is not None:
args.append(sample_x_stop)
if sample_y_step is not None:
args.append(sample_x_step)
if sample_y_start is not None or sample_y_stop is not None or sample_y_step is not None:
args.append(self.stage_y)
if sample_y_start is not None:
args.append(sample_y_start)
if sample_y_stop is not None:
args.append(sample_y_stop)
if sample_y_step is not None:
args.append(sample_y_step)
if args.count!=0:
args.append(self.pixium)
args.append(sample_exposure)
scan(args)
#sample_file_name = additional_plugin_list.getFullFileName()
scan_data_point_provider = InterfaceProvider.getScanDataPointProvider()
sample_file_name = scan_data_point_provider.getLastScanDataPoint().getCurrentFilename()
#builder = OSCommandRunnerBuilder.defaults()
builder = OSCommandRunnerBuilder.defaults()
builder=builder.command([LocalProperties.get("org.opengda.lde.pixium.data.reduction.script","/dls_sw/apps/i11-scripts/bin/LDE-RunFromGDAAtEndOfScan.sh"),self.calibrant_file_name])
builder=builder.keepOutput(True)
builder = builder.inputFilename(sample_file_name)
builder = builder.outputFilename(os.path.splitext(sample_file_name)[0]+"_output.log")
builder=builder.noTimeout()
builder.build()
from gdascripts.analysis.datasetprocessor.oned.MaxPositionAndValue import MaxPositionAndValue
from gdascripts.analysis.datasetprocessor.oned.MinPositionAndValue import MinPositionAndValue
from gdascripts.analysis.datasetprocessor.oned.CentreOfMass import CentreOfMass
from gdascripts.analysis.datasetprocessor.oned.GaussianPeakAndBackground import GaussianPeakAndBackground
from gdascripts.scan.process.ScanDataProcessor import ScanDataProcessor
from gdascripts.scan import specscans
from gdascripts.scan import gdascans
from gda.jython.commands.GeneralCommands import alias
from gda.jython import InterfaceProvider
from gda.scan import ScanDataPointCache
print "Setting up scan data point cache"
scanDataPointCache = ScanDataPointCache()
# Attach to JSF
InterfaceProvider.getScanDataPointProvider().addIScanDataPointObserver(scanDataPointCache)
print "Setting up scan data processor, scan_processor"
scan_processor = ScanDataProcessor([MaxPositionAndValue(), MinPositionAndValue(), CentreOfMass(), GaussianPeakAndBackground() ], globals(), scanDataPointCache=scanDataPointCache)
go = scan_processor.go
alias("go")
print "Creating spec-like commands:"
ascan = specscans.Ascan([scan_processor])
a2scan = specscans.A2scan([scan_processor])
a3scan = specscans.A3scan([scan_processor])
mesh = specscans.Mesh([scan_processor])
dscan = specscans.Dscan([scan_processor])
d2scan = specscans.D2scan([scan_processor])
d3scan = specscans.D3scan([scan_processor])
alias('ascan');print ascan.__doc__.split('\n')[3]
def __init__(self, level=logging.NOTSET):
logging.Handler.__init__(self, level)
self._printer = InterfaceProvider.getTerminalPrinter()
def isScanRunning(): return InterfaceProvider.getScanStatusHolder().getScanStatus() != JythonStatus.IDLE
def tomoScan(
description,
inBeamPosition,
outOfBeamPosition,
exposureTime=1.0,
start=0.0,
stop=180.0,
step=0.1,
darkFieldInterval=0,
flatFieldInterval=0,
imagesPerDark=10,
imagesPerFlat=10,
optimizeBeamInterval=0,
pattern="default",
tomoRotationAxis=0,
addNXEntry=True,
autoAnalyse=True,
additionalScannables=[],
):
"""
Function to collect a tomography step scan
Arguments:
description - description of the scan or the sample that is being scanned. This is generally user-specific information that may be used to map to this scan later and is available in the NeXus file)
inBeamPosition - position of X drive to move sample into the beam to take a projection
outOfBeamPosition - position of X drive to move sample out of the beam to take a flat field image
exposureTime - exposure time in seconds (default=1.0)
start - first rotation angle (default=0.0)
stop - last rotation angle (default=180.0)
step - rotation step size (default=0.1)
darkFieldInterval - number of projections between each dark-field sub-sequence.
NOTE: at least 1 dark is ALWAYS taken both at the start and end of the scan provided imagesPerDark>0
(default=0: use this value if you DON'T want to take any darks between projections)
flatFieldInterval - number of projections between each flat-field sub-sequence.
NOTE: at least 1 flat is ALWAYS taken both at the start and end the scan provided imagesPerFlat>0
(default=0: use this value if you DON'T want to take any flats between projections)
imagesPerDark - number of images to be taken for each dark-field sub-sequence (default=10)
imagesPerFlat - number of images to be taken for each flat-field sub-sequence (default=10)
General scan sequence is: D, F, P,..., P, F, D
where D stands for dark field, F - for flat field, and P - for projection.
"""
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
try:
darkFieldInterval = int(darkFieldInterval)
flatFieldInterval = int(flatFieldInterval)
optimizeBeamInterval = int(optimizeBeamInterval)
jns = beamline_parameters.JythonNameSpaceMapping(InterfaceProvider.getJythonNamespace())
tomography_theta = jns.tomography_theta
if tomography_theta is None:
raise "tomography_theta is not defined in Jython namespace"
tomography_shutter = jns.tomography_shutter
if tomography_shutter is None:
raise "tomography_shutter is not defined in Jython namespace"
tomography_translation = jns.tomography_translation
if tomography_translation is None:
raise "tomography_translation is not defined in Jython namespace"
tomography_detector = jns.tomography_detector
if tomography_detector is None:
raise "tomography_detector is not defined in Jython namespace"
tomography_optimizer = jns.tomography_optimizer
if tomography_optimizer is None:
raise "tomography_optimizer is not defined in Jython namespace"
tomography_time = jns.tomography_time
if tomography_time is None:
raise "tomography_time is not defined in Jython namespace"
tomography_beammonitor = jns.tomography_beammonitor
if tomography_beammonitor is None:
raise "tomography_beammonitor is not defined in Jython namespace"
tomography_camera_stage = jns.tomography_camera_stage
if tomography_camera_stage is None:
raise "tomography_camera_stage is not defined in Jython namespace"
tomography_sample_stage = jns.tomography_sample_stage
if tomography_sample_stage is None:
raise "tomography_sample_stage is not defined in Jython namespace"
tomo_additional_scannables = jns.tomography_additional_scannables
if tomo_additional_scannables is None:
raise "tomo_additional_scannables is not defined in Jython namespace"
index = SimpleScannable()
index.setCurrentPosition(0.0)
index.setInputNames(["imageNumber"])
index.setName("imageNumber")
index.configure()
image_key = SimpleScannable()
image_key.setCurrentPosition(0.0)
image_key.setInputNames(["image_key"])
image_key.setName("image_key")
image_key.configure()
tomoScanDevice = make_tomoScanDevice(
tomography_theta, tomography_shutter, tomography_translation, tomography_optimizer, image_key, index
)
# return tomoScanDevice
# generate list of positions
numberSteps = ScannableUtils.getNumberSteps(tomography_theta, start, stop, step)
theta_points = []
theta_points.append(start)
previousPoint = start
for i in range(numberSteps):
nextPoint = ScannableUtils.calculateNextPoint(previousPoint, step)
theta_points.append(nextPoint)
previousPoint = nextPoint
# generateScanPoints
optimizeBeamNo = 0
optimizeBeamYes = 1
shutterOpen = 1
shutterClosed = 0
shutterNoChange = 2
scan_points = []
theta_pos = theta_points[0]
index = 0
# Added shutterNoChange state for the shutter. The scan points are added using the (pseudo) ternary operator,
# if index is 0 then the shutterPosition is added to the scan point, else shutterNoChange is added to scan points.
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
) # dark
index = index + 1
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
) # flat
index = index + 1
scan_points.append((theta_pos, shutterOpen, inBeamPosition, optimizeBeamNo, image_key_project, index)) # first
index = index + 1
imageSinceDark = 1
imageSinceFlat = 1
optimizeBeam = 0
for i in range(numberSteps):
theta_pos = theta_points[i + 1]
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_project,
index,
)
) # main image
index = index + 1
imageSinceFlat = imageSinceFlat + 1
if imageSinceFlat == flatFieldInterval and flatFieldInterval != 0:
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
)
index = index + 1
imageSinceFlat = 0
imageSinceDark = imageSinceDark + 1
if imageSinceDark == darkFieldInterval and darkFieldInterval != 0:
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
)
index = index + 1
imageSinceDark = 0
optimizeBeam = optimizeBeam + 1
if optimizeBeam == optimizeBeamInterval and optimizeBeamInterval != 0:
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamYes,
image_key_project,
index,
)
)
index = index + 1
optimizeBeam = 0
# add dark and flat only if not done in last steps
if imageSinceFlat != 0:
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
) # flat
index = index + 1
if imageSinceDark != 0:
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
) # dark
index = index + 1
scan_points1 = generateScanPoints(
inBeamPosition,
outOfBeamPosition,
theta_points,
darkFieldInterval,
flatFieldInterval,
imagesPerDark,
imagesPerFlat,
optimizeBeamInterval,
pattern=pattern,
)
if pattern == "default" or pattern == "DFPFD":
i = 0
for pt1 in scan_points1:
pt = scan_points[i]
if pt1 != pt:
print "Mismatch - please tell Kaz about your scan and its arguments!"
print "i = ", i
print "pt = ", pt
print "pt1 = ", pt1
i += 1
# return None
positionProvider = tomoScan_positions(
start,
stop,
step,
darkFieldInterval,
imagesPerDark,
flatFieldInterval,
imagesPerFlat,
inBeamPosition,
outOfBeamPosition,
optimizeBeamInterval,
scan_points,
)
scan_args = [
tomoScanDevice,
positionProvider,
tomography_time,
tomography_beammonitor,
tomography_detector,
exposureTime,
tomography_camera_stage,
tomography_sample_stage,
]
# scan_args.append(RotationAxisScannable("approxCOR", tomoRotationAxis))
# meta_add(RotationAxisScannable("approxCOR", tomoRotationAxis))
# meta_add("RotationCoord_as_list", [tomoRotationAxis])
meta_add("approxCOR", tomoRotationAxis)
for scannable in additionalScannables:
scan_args.append(scannable)
for scannable in tomo_additional_scannables:
scan_args.append(scannable)
""" setting the description provided as the title"""
if not description == None:
setTitle(description)
else:
setTitle("undefined")
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
if not dataFormat == "NexusDataWriter":
handle_messages.simpleLog(
"Data format inconsistent. Setting 'gda.data.scan.datawriter.dataFormat' to 'NexusDataWriter'"
)
LocalProperties.set("gda.data.scan.datawriter.dataFormat", "NexusDataWriter")
scanObject = createConcurrentScan(scan_args)
if addNXEntry:
addNXTomoSubentry(scanObject, tomography_detector.name, tomography_theta.name)
scanObject.runScan()
if autoAnalyse:
lsdp = jns.lastScanDataPoint()
OSCommandRunner.runNoWait(
["/dls_sw/apps/tomopy/tomopy/bin/gda/tomo_at_scan_end", lsdp.currentFilename],
OSCommandRunner.LOGOPTION.ALWAYS,
None,
)
return scanObject
except InterruptedException:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "User interrupted the scan", exceptionType, exception, traceback, False)
raise InterruptedException("User interrupted the scan")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error during tomography scan", exceptionType, exception, traceback, False)
raise Exception("Error during tomography scan", exception)
finally:
handle_messages.simpleLog("Data Format reset to the original setting: " + dataFormat)
LocalProperties.set("gda.data.scan.datawriter.dataFormat", dataFormat)
