def __init__(self, name, idctrl, pgmenergy, lut="JIDEnergy2GapCalibrations.csv", energyConstant=False, polarisationConstant=False, gap_offset=None, feedbackPV=None):
'''Constructor - Only succeed if it find the lookupTable table, otherwise raise exception.'''
self.lut,self.header = load_lookup_table(LocalProperties.get("gda.config")+"/lookupTables/"+lut)
self.idscannable = idctrl
self.mono_energy = pgmenergy
self.scannables = ScannableGroup(name, [pgmenergy, idctrl])
self.detune = gap_offset
self.feedbackPV = feedbackPV
self._busy = 0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.setInputNames([name])
self.setExtraNames([])
self.polarisation = 'LH'
self.gap = 50
self.phase = 0
self.energyConstant = energyConstant
self.polarisationConstant = polarisationConstant
self.SCANNING = False
if self.energyConstant and self.polarisationConstant:
raise RuntimeError("Cannot create an instance with both energy and polarisation being constant.")
self.isConfigured = False
self.inputSignSwitched = False
self.beamlinename = LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME)
self.logger = logger.getChild(self.__class__.__name__)
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 __init__(self, name, idctrl, pgmenergy, lut="JIDEnergy2GapCalibrations.txt", energyConstant=False, polarisationConstant=False):
'''Constructor - Only succeed if it find the lookupTable table, otherwise raise exception.'''
self.lut=loadLookupTable(LocalProperties.get("gda.config")+"/lookupTables/"+lut)
self.idscannable=idctrl
self.pgmenergy=pgmenergy
self.scannables=ScannableGroup(name, [pgmenergy, idctrl])
self._busy=0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.setInputNames([name])
self.setExtraNames([])
self.order=1
self.polarisation=0.0
self.gap=50
self.polarisationMode='UNKNOWN'
self.phase=0
self.energyConstant=energyConstant
self.polarisationConstant=polarisationConstant
self.SCANNING=False
if self.energyConstant and self.polarisationConstant:
raise Exception("Cannot create an instance with both energy and polarisation being constant.")
self.isConfigured=False
self.inputSignSwitched=False
self.beamlinename=LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME)
self.logger = logger.getChild(self.__class__.__name__)
def setProperty(propertyName, propertyValue):
LocalProperties.set(propertyName, propertyValue)
eventAdmin=Finder.getInstance().find("eventadmin")
if eventAdmin is None:
print "Cannot find 'eventAdmin' on the GDA server. Please create a Spring bean using 'Scriptcontroller' Java class"
else:
eventAdmin.update(propertyName, propertyValue)
def prepareEmptyGdaVarFolder():
vartest_dir = os.path.join(os.getcwd(), 'var_test')
LocalProperties.set('gda.var', vartest_dir)
if os.path.exists(vartest_dir):
print "Removing existing gda.var: ", vartest_dir
shutil.rmtree(vartest_dir)
print "Creating gda.var: ", vartest_dir
os.mkdir(vartest_dir)
def prepareEmptyGdaVarFolder():
vartest_dir = os.path.join(os.getcwd(), 'var_test')
LocalProperties.set('gda.var', vartest_dir)
if os.path.exists(vartest_dir):
print "Removing existing gda.var: ", vartest_dir
shutil.rmtree(vartest_dir)
print "Creating gda.var: ", vartest_dir
os.mkdir(vartest_dir)
def setYFieldVisibleInScanPlot(indices=[-1]):
'''set the Y fields visible in Scan Plot using indices starting from 1.
this setting will be in effect as default until next update.
@param indices - a list of indices to be visible in the plot
GAD scan default is -1, means the last index
0 index means nothing visible
'''
LocalProperties.set("gda.plot.ScanPlotSettings.YFieldIndicesVisible",
":".join(map(str, indices)))
def datadir(newpath=None):
"""
Reads or sets the data directory. May also need to configure some detectors.
"""
if newpath==None:
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",None)
else:
if not os.path.exists(newpath):
raise ValueError("The directory %s does NOT exist!"%newpath)
print "Setting gda.data.scan.datawriter.datadir preference..."
LocalProperties.set("gda.data.scan.datawriter.datadir", newpath)
# Save to localShelf
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",None)
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 __getGdaModeProperty():
mode = str(LocalProperties.get("gda.mode"))
if mode not in ("live", "dummy", "simulation"):
raise ValueError(
"gda.mode LocalProperty (perhaps via a System property) must be 'live' or 'dummy' not:",
mode)
return mode
def getYFieldVisibleInScanPlot():
'''return the indices of the current Y fields visible in Scan Plot
-1 means the last index
0 means no visible data trace
'''
return LocalProperties.getAsIntList(
"gda.plot.ScanPlotSettings.YFieldIndicesVisible")
def loadEnergyFocus():
stashFilePath = LocalProperties.get(
"gda.var") + "/energyFocusFunction.json"
print("Loading energy/focus parameters from " + abspath(stashFilePath))
try:
stashFile = open(stashFilePath, 'r')
stashedValue = json.load(stashFile)
stashFile.close()
slopeDividend = stashedValue.get('slopeDividend')
interception = stashedValue.get('interception')
slopeDivisor = stashedValue.get('slopeDivisor')
except:
print("Cannot load stored energy focus values from " +
abspath(stashFilePath) + ", using defaults")
slopeDividend = u'0.0 µm'
interception = u'0.0 µm'
slopeDivisor = '1.0 eV'
energyFocusFunction.setSlopeDividend(
QuantityFactory.createFromString(slopeDividend))
energyFocusFunction.setInterception(
QuantityFactory.createFromString(interception))
energyFocusFunction.setSlopeDivisor(
QuantityFactory.createFromString(slopeDivisor))
print("energyFocusFunction set to: " + energyFocusFunction.toString())
def setDir(proposal=None, visit=1):
#get beamline name from GDA propertie
#beamlineName = LocalProperties.get("gda.instrument");
beamlineName = LocalProperties.get("gda.beamline.name")
commissioningProposal = bpDict.get(beamlineName, 'unknownPorposal')
if proposal is None: # the default commissioning proposal
proposal = commissioningProposal
userDir = proposal + "-" + str(visit)
#get current Year
currentTime = localtime()
currentYear = currentTime[0]
userDir = "/dls/" + beamlineName + "/data/" + str(
currentYear) + "/" + userDir
symbolicLink = "/dls/" + beamlineName + "/data/operation"
print "New user data directory is: " + userDir
#remove the old symbolic link
system("rm -f " + symbolicLink)
#create the new symbolic link to point to the user data directory
system("ln -s " + userDir + " " + symbolicLink)
def datadir(newpath=None):
"""
Reads or sets the data directory. May also need to configure some detectors.
"""
if newpath == None:
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",
None)
else:
if not os.path.exists(newpath):
raise ValueError("The directory %s does NOT exist!" % newpath)
print "Setting gda.data.scan.datawriter.datadir preference..."
LocalProperties.set("gda.data.scan.datawriter.datadir", newpath)
# Save to localShelf
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",
None)
def setDir(proposal, visit, LocalProperties=LocalProperties):
#get beamline name from GDA propertie
#beamlineName = LocalProperties.get("gda.beamline.name");
beamlineName = LocalProperties.get("gda.instrument.name");
commissioningProposal = bpDict.get(beamlineName, 'unknownPorposal');
if proposal == commissioningProposal: # the default commissioning proposal
userDir = proposal;
else:
userDir = proposal + "-" + str(visit);
#get current Year
currentTime = time.localtime();
currentYear = currentTime[0];
userDir="/dls/" + beamlineName + "/data/" + str(currentYear) + "/" + userDir;
symbolicLink = "/dls/" + beamlineName + "/data/operation";
print "New user data directory is: " + userDir;
#remove the old symbolic link
os.system("rm -f " + symbolicLink);
#create the new symbolic link to point to the user data directory
os.system("ln -s " + userDir + " " + symbolicLink);
def __init__(self,
name,
idgap,
dcmenergy,
lut,
gap_offset=None,
feedbackPVs=None):
"""
Constructor - Only succeeds if it finds the lookup table,
otherwise raises exception.
"""
self.lut = readLookupTable(
LocalProperties.get("gda.config") + "/lookupTables/" + lut)
self.gap = idgap
self.mono_energy = dcmenergy
self.lambdau = 27 # undulator period
self.scannables = ScannableGroup(name, [dcmenergy, idgap])
self.detune = gap_offset
self.feedbackPVs = feedbackPVs
self._busy = 0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.inputNames = [name]
self.order = 3
self.SCANNING = False
self.logger = logger.getChild(self.__class__.__name__)
def reload(self, commandServer):
self.commandServer = commandServer
self.jythonNamespaceMapping = {}
self.jythonNamespaceMapFilePath = LocalProperties.get(
JYTHON_NAMESPACE_MAPPING_FILE_PROPERTY)
if (self.jythonNamespaceMapFilePath != None):
self.jythonNamespaceMapping = readDictionaryFromFile(
self.jythonNamespaceMapFilePath, self.jythonNamespaceMapping)
def reload(self, finder):
self.finder = finder
self.finderNameMapping = {}
self.finderNameMapFilePath = LocalProperties.get(
FINDER_NAME_MAPPING_FILE_PROPERTY)
if (self.finderNameMapFilePath != None):
self.finderNameMapping = readDictionaryFromFile(
self.finderNameMapFilePath, self.finderNameMapping)
def dataCollection(samples=[]):
lookuptable=readLookupTable(LocalProperties.get("gda.function.lookupTable.dir")+os.path.sep+"lde_stages_home_positions.txt")
for each in lookuptable.keys:
stage=StageDataCollection(each)
for sample in samples:
if sample["cell_ID"].contains(each):
stage.addSample(sample)
stage.processSamples()
def __init__(self, stageName):
self.name=stageName
self.calibrant_file_name=None
self.stage_x=Finder.getInstance().find(stageName+"x")
self.stage_y=Finder.getInstance().find(stageName+"y")
self.stage_rot=Finder.getInstance().find(stageName+"rot")
self.lookup_table = readLookupTable(LocalProperties.get("gda.function.lookupTable.dir")+os.path.sep+"lde_stages_home_positions.txt")
self.samples=[]
self.calibration_required=True
self.pixium=Finder.getInstance().find('pixium_hdf')
def __init__(self, name):
logger.debug("Camera Setup")
self.pin = -1
self.device = name
self.setName(name)
self.currentPosition = 0
self.lastPosition = 0 # required
self.busyStatus = False
beamlineName = LocalProperties.get("gda.beamline.name")
self.numTracker = data.NumTracker(beamlineName)
rpiComms.rpiCommunicator.scannables.append(self)
def reload(self, parametersFilePath=None):
if parametersFilePath == None:
self.parametersFilePath = LocalProperties.get(
BEAMLINE_PARAMETERS_FILE_PROPERTY)
if (self.parametersFilePath == None):
raise AttributeError, "property " + BEAMLINE_PARAMETERS_FILE_PROPERTY + " is not set"
else:
self.parametersFilePath = parametersFilePath
self.parameters = {}
self.parameters = readDictionaryFromFile(self.parametersFilePath,
self.parameters)
def __init__(self, name):
logger.debug("Camera Setup")
self.pin = -1
self.device = name
self.setName(name)
self.currentPosition = 0
self.lastPosition = 0 # required
self.busyStatus = False
beamlineName = LocalProperties.get("gda.beamline.name")
self.numTracker = data.NumTracker(beamlineName)
rpiComms.rpiCommunicator.scannables.append(self)
def __init__(self, name): #setup stuff
logger.debug("Camera Setup")
#self.pin = -1
self.device = name
self.setName(
name) #this is setting up the name passed in localstation.py
self.currentPosition = 0
self.lastPosition = 0 # required
self.busyStatus = False
beamlineName = LocalProperties.get("gda.beamline.name")
self.numTracker = data.NumTracker(beamlineName)
print "camera setup"
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 loadsampleinformationfile(filename, LocalProperties=LocalProperties):
"""Load sample information from users provided Excel spreadsheet into GDA system.
usage:
loadsampleinformationfile('/absolute/File/Path/To/Excel/Spreadsheet')
"""
vardir = LocalProperties.get("gda.config") + "/var";
defaulfFilename = vardir + "/SampleInfo.xls";
#copy user supplied file over to GDA system
val=os.system("cp -f " + filename + " " + defaulfFilename);
if val == 0:
print "load completed."
else:
raise Exception("File load failed.")
# health check on file read/write permissions
si.setSampleInfoFile(defaulfFilename) #@UndefinedVariable
def __init__(self, name, lut):
"""
Constructor - Only succeeds if it finds the lookup table,
otherwise raises exception.
"""
self.lut = readLookupTable(
LocalProperties.get("gda.config") + "/lookupTables/" + lut)
self.gap = "igap"
self.dcm = "dcmenergy"
self.lambdau = 27 # undulator period
self.scannableNames = ["dcmenergy", "igap"]
self.scannables = ScannableGroup(
name, [Finder.find(x) for x in self.scannableNames])
self._busy = 0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.inputNames = [name]
self.order = 3
self.logger = logger.getChild(self.__class__.__name__)
def getDir(proposal, visit, LocalProperties=LocalProperties):
#get beamline name from GDA propertie
#beamlineName = LocalProperties.get("gda.beamline.name");
beamlineName = LocalProperties.get("gda.instrument.name");
commissioningProposal = bpDict.get(beamlineName, 'unknownPorposal');
if proposal == commissioningProposal: # the default commissioning proposal
userDir = proposal;
else:
userDir = proposal + "-" + str(visit);
#get current Year
currentTime = time.localtime();
currentYear = currentTime[0];
userDir="/dls/" + beamlineName + "/data/" + str(currentYear) + "/" + userDir;
symbolicLink = "/dls/" + beamlineName + "/data/operation";
print userDir + " is the user data directory for this proposal and visit.";
def __init__(self, name, idgap, pgmenergy, lut, gap_offset=None, feedbackPV=None):
"""
Constructor -
Only succeeds if it finds the lookup table, otherwise raises exception.
"""
self.lut = readLookupTable(LocalProperties.get("gda.config") + "/lookupTables/" + lut)
self.gap = idgap
self.mono_energy = pgmenergy
self.scannables = ScannableGroup(name, [pgmenergy, idgap])
self.detune=gap_offset
self.feedbackPV=feedbackPV
self._busy = 0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.inputNames = [name]
self.SCANNING=False
self.order = 1
self.polarisation = 'LH'
self.jidphase = Finder.find("jidphase")
self.logger = logger.getChild(self.__class__.__name__)
def __init__(self, name, gap="jgap", dcm="pgmenergy", undulatorperiod=27, lut="JIDCalibrationTable.txt"):
'''Constructor - Only succeed if it find the lookup table, otherwise raise exception.'''
self.lut=readLookupTable(LocalProperties.get("gda.config")+"/lookupTables/"+lut)
self.gap=gap
self.dcm=dcm
self.lambdau=undulatorperiod
if dcm is None:
self.scannableNames=[gap]
else:
self.scannableNames=[dcm,gap]
self.scannables=ScannableGroup(name, [Finder.find(x) for x in self.scannableNames])
self._busy=0
self.setName(name)
self.setLevel(3)
self.setOutputFormat(["%10.6f"])
self.inputNames=[name]
if self.dcm == "dcmenergy":
self.order=3
else:
self.order=1
self.energy=self.scannables.getGroupMember(self.scannableNames[0]).getPosition()
self.polarisation='H'
def getDir(proposal, visit, LocalProperties=LocalProperties):
#get beamline name from GDA propertie
#beamlineName = LocalProperties.get("gda.beamline.name");
beamlineName = LocalProperties.get("gda.instrument.name")
commissioningProposal = bpDict.get(beamlineName, 'unknownPorposal')
if proposal == commissioningProposal: # the default commissioning proposal
userDir = proposal
else:
userDir = proposal + "-" + str(visit)
#get current Year
currentTime = time.localtime()
currentYear = currentTime[0]
userDir = "/dls/" + beamlineName + "/data/" + str(
currentYear) + "/" + userDir
symbolicLink = "/dls/" + beamlineName + "/data/operation"
print userDir + " is the user data directory for this proposal and visit."
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()
def getDataWriter():
return LocalProperties.get("gda.data.scan.datawriter.dataFormat")
def setDataWriterToSrs():
oldDW = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
LocalProperties.set("gda.data.scan.datawriter.dataFormat", "SrsDataFile")
newDW = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
print "Old DataWriter: ", oldDW
print "New DataWriter: ", newDW
fileHeader = MetadataHeaderDeviceClass("fileHeader")
import __main__ # @UnresolvedImport
blList = [__main__.beamenergy, __main__.ringcurrent]
fileHeader.add(blList)
#bpmList= [xbpm1x, xbpm1y, xbpm2x, xbpm2y, xbpm1anglex, xbpm1angley]; fileHeader.add(bpmList);
idList = [
__main__.iddgap, __main__.iddtrp, __main__.iddbrp, __main__.idugap,
__main__.idutrp, __main__.idubrp, __main__.pugap
]
fileHeader.add(idList)
beamline = LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME)
if installation.isLive() and beamline != "lab44":
pgmList = [
__main__.pgmpitch, __main__.pgmgratpitch, __main__.cff,
__main__.grating, __main__.pgmenergy
]
else:
#grating requires EPICS access
pgmList = [
__main__.pgmpitch, __main__.pgmgratpitch, __main__.cff,
__main__.pgmenergy
]
fileHeader.add(pgmList)
'''
Created on 29 Jan 2014
@author: fy65
'''
from time import sleep
from gda.configuration.properties import LocalProperties
from gda.data import NumTracker
scanNumTracker=NumTracker(LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME))
scanNumTracker.incrementNumber()
EXPOSURETIME=120 #seconds
TARGETCOUNT=100000
ONEMINUTECOUNT=1000
DELTAMIN=-15.0
DELTAMAX=77.0
scancount=0
Tolerance=0.1
NUMBEROFSCANS=TARGETCOUNT/ONEMINUTECOUNT*60/EXPOSURETIME
print "Number of scans to do: %d, total time taken: %f" % (NUMBEROFSCANS, NUMBEROFSCANS*EXPOSURETIME)
mythen.configure() # @UndefinedVariable
mythen.atScanStart() # @UndefinedVariable
mythen.setCollectionTime(EXPOSURETIME+10) # @UndefinedVariable
delta.moveTo(DELTAMIN) # @UndefinedVariable
delta.setSpeed((DELTAMAX-DELTAMIN)/(EXPOSURETIME)) # @UndefinedVariable
target=DELTAMAX
for i in range(NUMBEROFSCANS):
sleep(5)
if scancount % 2==0:
target=DELTAMAX
else:
"""Utility script to help manage BSL file conversion"""
from gda.configuration.properties import LocalProperties
from gda.factory import Finder
from gda.observable import IObserver
from uk.ac.diamond.daq.persistence.jythonshelf import LocalParameters
from gda.data.metadata import GDAMetadataProvider
BSL_CONVERSION_CONFIGURED = 'gda.scan.processing.bsl.configured'
RUNNER = Finder.getInstance().find('bslConversion')
class BslConversionUpdater(IObserver):
def update(self, source, arg):
print 'Visit changed to ' + str(arg)
restore()
if not LocalProperties.contains(BSL_CONVERSION_CONFIGURED):
LocalProperties.set(BSL_CONVERSION_CONFIGURED, 'True')
for meta in GDAMetadataProvider.getInstance().getMetadataEntries():
if meta.name == 'visit':
break
if meta:
meta.addIObserver(BslConversionUpdater())
CONFIGURATION_FILE = 'bslUsers'
DEFAULT = False
STORE = LocalParameters.getXMLConfiguration(CONFIGURATION_FILE)
def isConvertingOn():
"""Check whether new files will be converted automatically"""
from gda.device.scannable.scannablegroup import ScannableGroup
from gdascripts.scannable.dummy import SingleInputDummy as Dummy
from diffcmd.diffcmd_utils import alias_commands
GDA = True
except ImportError:
# Not running in gda environment so fall back to minigda emulation
from diffcalc.gdasupport.minigda.scannable import ScannableGroup
from diffcalc.gdasupport.minigda.scannable import SingleFieldDummyScannable as Dummy
GDA = False
HELP_STRING = \
"""Quick: https://github.com/DiamondLightSource/diffcalc/blob/master/README.rst
Manual: http://diffcalc.readthedocs.io/en/latest/youmanual.html
Type: > help ub
> help hkl"""
if GDA:
from gda.configuration.properties import LocalProperties
var_folder = LocalProperties.get("gda.var")
diffcalc_persistance_path = os.path.join(var_folder, 'diffcalc')
if not os.path.exists(diffcalc_persistance_path):
print "Making diffcalc var folder:'%s'" % diffcalc_persistance_path
os.makedirs(diffcalc_persistance_path)
settings.ubcalc_persister = UBCalculationJSONPersister(diffcalc_persistance_path)
# else: should have been set if outside GDA
# See notes in: http://wiki.diamond.ac.uk/Wiki/Wiki.jsp?page=I06_Diffcalc
try:
import diffcalc
except ImportError:
from gda.configuration.properties import LocalProperties
import sys
diffcalc_path = LocalProperties.get(
"gda.install.git.loc") + '/diffcalc.git'
sys.path = [diffcalc_path] + sys.path
print diffcalc_path + ' added to GDA Jython path.'
import diffcalc
from gdascripts.pd.dummy_pds import DummyPD
from diffcalc.gdasupport.factory import create_objects, add_objects_to_namespace
CREATE_DUMMY_AXES = False
if CREATE_DUMMY_AXES:
print "!!! Starting dummy diffcalc with tth, th, chi, phi and en."
tth = DummyPD('tth')
th = DummyPD('th')
en = DummyPD('en')
en(1500)
diffcalc_energy = en
else:
print "!!! Starting LIVE diffcalc with th(dd2th), th(ddth), chi(dummy), phi(dummy) and denergy."
tth = dd2th
th = ddth
diffcalc_energy = denergy
chi = DummyPD('chi')
import sys
from gda.jython import InterfaceProvider
from gda.jython.commands.GeneralCommands import alias
from Diamond.Utility.UtilFun import UtilFunctions
from Diamond.Utility.BeamlineFunctions import BeamlineFunctionClass, logger
from Diamond.PseudoDevices.FastEnergyScan import FastEnergyScanControlClass, FastEnergyScanIDModeClass
from Diamond.PseudoDevices.FastEnergyScan import FastEnergyDeviceClass
#from Diamond.PseudoDevices.FastEnergyScan import EpicsScandataDeviceClass;
from Diamond.PseudoDevices.FastEnergyScan import EpicsWaveformDeviceClass
from gda.configuration.properties import LocalProperties
uuu = UtilFunctions()
beamline_name = LocalProperties.get(LocalProperties.GDA_BEAMLINE_NAME, "i06")
beamlineutil = BeamlineFunctionClass(beamline_name)
# Change rootPV to switch zacscan between IDs. (search for "switch zacscan" to find other changes needed)
rootPV = "BL06J-MO-FSCAN-01"
fastScanElementCounter = "iddFastScanElementCounter"
#rootPV = "BL06J-MO-FSCAN-02";
#fastScanElementCounter="iduFastScanElementCounter"
fesController = FastEnergyScanControlClass("fesController", rootPV)
zacmode = FastEnergyScanIDModeClass("zacmode", fesController)
#fesData = EpicsScandataDeviceClass("fesData", rootPV);
fesData = EpicsWaveformDeviceClass(
"fesData",
rootPV, ['C1', 'C2', 'C3', 'C4', 'iddenergy', 'pgmenergy', 'C5', 'C6'],
['idio', 'ifio'],
elementCounter=fastScanElementCounter)
'''
Scannable defines the X-ray source mode to be one of ['idd','idu','dpu','dmu'] in GDA only.
It enables and disable 'zacscan' support when sets the mode value.
Created on 13 Apr 2017
@author: fy65
'''
from gda.device.scannable import ScannableBase
from gda.configuration.properties import LocalProperties
from time import sleep
from gda.jython.commands import GeneralCommands
from i06shared import installation
gda_git_loc = LocalProperties.get(LocalProperties.GDA_GIT_LOC)
class SourceMode(ScannableBase):
'''
implements the 4 X-ray beam source modes
1. Single operation of HU64a - specified by value 'idd'
2. Single operation of HU64b - specified by value 'idu'
3. Operation of HU64a and HU64b in the same polarisation - specified by value 'dpu'
4. Operation of HU64a and HU64b, but with different polarisations - specified by value 'dmu'
Instance of this Scannable set/get source mode value in GDA only which
- enables 'zacscan' for the single source modes - 'idd' and 'idu'
- disables 'zacscan' for combined source modes - 'dpu' and 'dmu'
'''
SOURCE_MODES = ['idd', 'idu', 'dpu', 'dmu', 'unknown']
'''
Created on 17 Apr 2018
@author: fy65
'''
from gda.configuration.properties import LocalProperties
lookup_tables_dir = LocalProperties.get("gda.function.lookupTable.dir")
def isLive():
mode = LocalProperties.get("gda.mode")
return mode =="live"
def FindScanPeak2(ordinateName, printNameList=[], abscissaNameList=[], scanID=0, peakRatio=-1, ToPrint=1, LocalProperties=LocalProperties):
""" Values= FindScanPeak(ordinateName, printNameList=[], scanID='null', ToPrint=1)
Finds the peak value within a scan (currently just the maximum value). Returns all
values from this line as dictionary. If enabled prints some values from this line.
Will return only a peak that extends at least peakRatio*noise_rate above the Poisson noise floor. If no
peak large enougth exists then Values returned is empty.
Keyword arguements:
ordinateName -- the header name of the value whose peak is to be found
printNameList -- a list of header names to print (if enabled),
abscissaNameList -- NOT USED. may later be used for more advanced peak finding algorithms
scanID -- leave empty to read most recent scan. Else a scan number or an absolute
file path. If negative (-n), will find the peak of the scan n scans old.
peakRatio -- If non-negative, this is the factor that a peak must extend above the Poisson noise floor to count.
i.e. (peakValue-noise) >= peakRatio*noise, where noise is the avergae poisson noise floor.
Be warned that the measured poisson noise floor is calculated without accounting
for any real signal that may be present, so will be an overestimate.
ToPrint -- Set to 0 to disable printing
Returns:
The values of all elements from the selected line in a dictionary with header
names as keys (or an empty dictionary if peakRatio is ser, and no peak was found)
Example:
run FindScanPeak (as import is dodgy!)
peakValues = FindScanPeak("y", ["x","y"], scanID = 15) #loads scan number 15, finds the maximum y,
prints x and y, and returns all values.
peakValues = FindScanPeak("y", ["x","y"], peakRatio=5) #loads the most recent scan and finds the maximum
y if it large enougth, prints x and y, and returns all values.
"""
# ----- Generate path -----
# Use scanID as path if it is a string
if type(scanID) == type('gda rocks'):
filepath = scanID
else: # Assemble a path from the scan number, using current scan if not given
# If no scanID given, use current scan number
if scanID <= 0:
import gda.data.NumTracker
numtracker = gda.data.NumTracker('tmp')
scanID = numtracker.getCurrentFileNumber() + scanID
# Implicit else: scanID must be a positive number
# scanID now contains the number of a scan
filepath = LocalProperties.get("gda.data.scan.datawriter.datadir")
filepath = filepath + '/' + str(scanID) + '.dat'
if ToPrint == 1:
print "In file: %s" % filepath
# ----- Read the file -----
(headerList, columnList) = readSRSDataFile(filepath)
# ----- Turn these into dictionary objects with header names as keys -----
dataDict = {}
for i in range(0, len(headerList)):
dataDict[headerList[i]]=columnList[i]
# ----- Find the index of the point -----
iPeak = findMaxPointNonInterp(dataDict[ordinateName])
# Get the value of the peak
tempList = dataDict[ordinateName]
peakValue = tempList[iPeak]
# ----- Calculate statistics -----
y_array = dataDict[ordinateName]
calc_noPoints = len(y_array)
# Normal distribution statistics
calc_mean = average(y_array)
calc_stdDev = standardDeviation(y_array)
# Poisson distribution statistics
calc_lambda = calc_mean
calc_poisson_stddev = math.sqrt(calc_lambda)
# Threshold based on Poisson statistics
calc_threshold = peakRatio*calc_poisson_stddev + calc_lambda
# ----- Print some stuff unless ToPrint passed in as 0 -----
if ToPrint == 1:
print "Max %s occurs at point %i (starting from 0) where:" % (ordinateName, iPeak)
for i in range(0, len(printNameList)):
tempList = dataDict[printNameList[i]]
print "%s = %f" % (printNameList[i],tempList[iPeak])
print ""
if (peakRatio >=0): # Show statistics as a peak threshold exists
print "Number points: %i" % calc_noPoints
print "Normal:\tmean: %f \t stddev: %f" % ( calc_mean, calc_stdDev)
print "Poisson:\tlambda: %f \t stddev(noise): %f" % ( calc_lambda, calc_poisson_stddev)
print "Threshold (%f*%f+%f) is:%f" % (peakRatio, calc_poisson_stddev, calc_lambda, calc_threshold)
if peakValue>=calc_threshold:
print "*Peak found*: The peak value of %f is greater than the threshold" % peakValue
else:
print "*No peak found* The peak value of %f less than the threshold" % peakValue
# ----- Return a dict object of values line where max occured -----
# If threshold is exceeded...
if ((peakValue>=calc_threshold) or peakRatio<0):
maxPeak = {}
for i in range(0, len(headerList)):
tempList = dataDict[headerList[i]]
maxPeak[headerList[i]] = tempList[iPeak]
return maxPeak
else: # Return an empty dictionary
return {}
from gda.oe import OE
from gda.oe.dofs import DOF
from gda.device import ScannableMotion
from gda.oe import OE
from gda.device.epicsdevice import IEpicsDevice
from gda.util.converters import IReloadableQuantitiesConverter
# Channel access commands
from gda.epics import CAClient
from gda.epics.CAClient import *
from org.pf.joi import Inspector
# Get the location of the GDA beamline script directory
from gda.configuration.properties import LocalProperties
LocalProperties=LocalProperties
gdaScriptDir = LocalProperties.get("gda.jython.gdaScriptDir")
gdaScriptDir = gdaScriptDir + "/"
userScriptDir = LocalProperties.get("gda.jython.userScriptDir")
userScriptDir = userScriptDir + "/"
commonScriptDir = LocalProperties.get("gda.jython.commonScriptDir")
commonScriptDir = commonScriptDir + "/"
# we need all OEs and their DOFs to be available in the
# namespace, by wrapping references to them in Adapter objects
finder = Finder.getInstance()
OEs = []
DOFs=[]
OEs = finder.listAllNames("OE");
for fullName in OEs:
objRef = finder.find(fullName)
# create an OE adapter object
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 parkingAllDevices():
'''move all stages to parking positions'''
lookuptable=readLookupTable(LocalProperties.get("gda.function.lookupTable.dir")+os.path.sep+"lde_stages_home_positions.txt")
for each in lookuptable.keys:
stage=StageDataCollection(each)
stage.moveToSafePosition()
# alias("createPVScannable")
# alias("caput")
# alias("caget")
from gda.scan.RepeatScan import create_repscan, repscan
vararg_alias("repscan")
#setup tools to create metadata in Nexus files
from gdascripts.metadata.metadata_commands import setTitle, meta_add, meta_ll, meta_ls, meta_rm
alias("setTitle")
alias("meta_add")
alias("meta_ll")
alias("meta_ls")
alias("meta_rm")
from gda.data.scan.datawriter import NexusDataWriter
LocalProperties.set(NexusDataWriter.GDA_NEXUS_METADATAPROVIDER_NAME,"metashop")
#create time scannables
from gdascripts.pd.time_pds import waittimeClass2, showtimeClass, showincrementaltimeClass, actualTimeClass
waittime=waittimeClass2('waittime')
showtime=showtimeClass('showtime')
inctime=showincrementaltimeClass('inctime')
actualTime=actualTimeClass("actualTime")
#===================================================
#Raspberry Pi Specific Objects
#===================================================
#RPi Communication Interface
#rpiComms.initaliseCommunicator("127.23.31.56") #enter the Pi's IP address, 127.0.0.1 (localhost) should work
#PiCamera Interface
alias("createPVScannable")
alias("caput")
alias("caget")
from gda.scan.RepeatScan import create_repscan, repscan
vararg_alias("repscan")
#setup tools to create metadata in Nexus files
from gdascripts.metadata.metadata_commands import setTitle, meta_add, meta_ll, meta_ls, meta_rm
alias("setTitle")
alias("meta_add")
alias("meta_ll")
alias("meta_ls")
alias("meta_rm")
from gda.data.scan.datawriter import NexusDataWriter
LocalProperties.set(NexusDataWriter.GDA_NEXUS_METADATAPROVIDER_NAME,"metashop")
#create time scannables
from gdascripts.pd.time_pds import waittimeClass2, showtimeClass, showincrementaltimeClass, actualTimeClass
waittime=waittimeClass2('waittime')
showtime=showtimeClass('showtime')
inctime=showincrementaltimeClass('inctime')
actualTime=actualTimeClass("actualTime")
#run user editable startup script
if isLive():
run("localStationUser.py")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error in localStation", exceptionType, exception, traceback, False)
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)
def isLive():
mode = LocalProperties.get("gda.mode")
return mode =="live"
