def visit(self, new_visit = None):
if new_visit:
Finder.getInstance().find("GDAMetadata").setMetadataValue("visit", new_visit)
Finder.getInstance().find("GDAMetadata").setMetadataValue("defaultVisit", new_visit)
if not os.path.exists(self.getVisitDirectory()):
print "!!! Warning !!! The directory '%s' does NOT exist! (pointing to it anyway though)" %self.getVisitDirectory()
self.setDetectorDirectories()
return Finder.getInstance().find("GDAMetadata").getMetadataValue("visit")
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 visit(self, new_visit=None):
if new_visit:
Finder.getInstance().find("GDAMetadata").setMetadataValue(
"visit", new_visit)
Finder.getInstance().find("GDAMetadata").setMetadataValue(
"defaultVisit", new_visit)
if not os.path.exists(self.getVisitDirectory()):
print "!!! Warning !!! The directory '%s' does NOT exist! (pointing to it anyway though)" % self.getVisitDirectory(
)
self.setDetectorDirectories()
return Finder.getInstance().find("GDAMetadata").getMetadataValue(
"visit")
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 __init__(self, name, tfg, fg, adc, pe, detector):
self.name=name
self.tfg=tfg
self.fg=fg
self.adc=adc
self.pedata=pe
self.detector=detector
self.fastshutter=Finder.getInstance().find("fastshutter")
self.numGates=1
self.numCycles=1
self.numFrames=1
self.livetime=0.0
self.deadtime=0.0
self.boundaryFrequency=0.1
self.func = 2
self.bncycle=1
self.freq=0.1
self.adcStreamerCompleted=True
self.gateDetectorCompleted=True
self.numDefinedSequency=1
self.filename=""
self.directory=""
self.scanNumber=0
self.preConditioning=True
self.startCycleNumber=0
self.startSeqNumber=0
def Assemble(self):
nameList=Finder.getInstance().listAllNames('Scannable')
nameList=['ab__a', 'ab__b', 'xyz__x', 'xyz__y', 'xyz__z', 'blarghh']
# Filter out those containing __
groupComponentList=[]
for name in nameList:
if name.__contains__('__'):
groupComponentList.append(name)
# Create a dictionary with one key for each group, each key pointing to a list of component strings"
groupDict={}
for name in groupComponentList:
group, component = name.split('__')
if not(groupDict.has_key(group)):
groupDict[group]=[]
groupDict[group].append(component)
# Create the group scannables and pass back as list (STUB)
toReturn = []
groupNameList = groupDict.keys()
for groupName in groupNameList:
tmp=groupName
for componentName in groupDict[groupName]:
tmp += "." + componentName
toReturn += [tmp]
return toReturn
def getUserOptionsManager(): manager = Finder.getInstance().findSingleton(UserOptionsManager) if not manager: manager = UserOptionsManager() manager.configure() return manager
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 Assemble(self):
nameList = Finder.getInstance().listAllNames('Scannable')
nameList = ['ab__a', 'ab__b', 'xyz__x', 'xyz__y', 'xyz__z', 'blarghh']
# Filter out those containing __
groupComponentList = []
for name in nameList:
if name.__contains__('__'):
groupComponentList.append(name)
# Create a dictionary with one key for each group, each key pointing to a list of component strings"
groupDict = {}
for name in groupComponentList:
group, component = name.split('__')
if not (groupDict.has_key(group)):
groupDict[group] = []
groupDict[group].append(component)
# Create the group scannables and pass back as list (STUB)
toReturn = []
groupNameList = groupDict.keys()
for groupName in groupNameList:
tmp = groupName
for componentName in groupDict[groupName]:
tmp += "." + componentName
toReturn += [tmp]
return toReturn
def meta_add( farg, *vargs):
"""
Command to add a scannable to the items to be put into the scan metadata
"""
metashop=Finder.getInstance().find("metashop")
if metashop == None:
return
metashop.add([farg]+list(vargs))
def __init__(self, name, scannableX, scannableY, deviceFun):
"""constructor parameters:
name: Name of the new device
scannableX: Name of the scannable on X-axis (for example: "energy")
scannableY: Name of the scannable on Y-axis (for example: "mac15")
deviceFun: Name of the function to calculate the new position based on scannableX and scannableY positions"""
self.setName(name)
self.setInputNames([name])
# self.Units=[strUnit]
# self.setOutputFormat([strFormat])
# self.setLevel(8);
self.x1 = 0.0
self.x2 = 0.0
self.y = 0.0
self.refObj1 = Finder.getInstance().find(scannableX)
self.refObj2 = Finder.getInstance().find(scannableY)
self.deviceFun = deviceFun
def meta_rm(farg, *vargs):
"""
Command to remove items to be put into the scan metadata.
"""
metashop=Finder.getInstance().find("metashop")
if metashop == None:
return
metashop.remove([farg]+list(vargs))
def meta_rm(farg, *vargs):
"""
Command to remove items to be put into the scan metadata.
"""
metashop = Finder.getInstance().find("metashop")
if metashop == None:
return
metashop.remove([farg] + list(vargs))
def meta_add(farg, *vargs):
"""
Command to add a scannable to the items to be put into the scan metadata
"""
metashop = Finder.getInstance().find("metashop")
if metashop == None:
return
metashop.add([farg] + list(vargs))
def runExperiment(self):
print "I am now running the experiment using parameters in the bean",str(self.bean),"..."
time.sleep(2)
print "...and now the experiment is over."
scriptController = Finder.getInstance().find("MyExperimentScriptController")
if scriptController != None:
print "Broadcasting experiment complete message..."
scriptController.update("MyExperiment Script", "Experiment Complete!")
def _createHeaderStringForScannables(self, fmt='%s=%s\n'):
s = ""
metascannables = Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
for scn in metascannables:
pairs = self._createNamePositionPairs(scn)
for key, value in pairs:
s += fmt % (key, value)
return s
def _createHeaderStringForScannables(self, fmt='%s=%s\n'):
s = ""
metascannables = Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
for scn in metascannables:
pairs = self._createNamePositionPairs(scn)
for key, value in pairs:
s += fmt % (key, value)
return s
def reloadLookupTables():
"""reloads all lookup tables on the ObjectServer"""
controller = None
prefix = "reloadLookupTables:"
update(controller, prefix, " - started.")
finder = Finder.getInstance()
converters = finder.listAllObjects("IReloadableQuantitiesConverter")
for converter in converters:
update(controller, prefix, "..." + converter.getName() )
converter.reloadConverter()
update(controller, prefix, " - completed")
def runExperiment(self):
print "I am now running the experiment using parameters in the bean", str(
self.bean), "..."
time.sleep(2)
print "...and now the experiment is over."
scriptController = Finder.getInstance().find(
"MyExperimentScriptController")
if scriptController != None:
print "Broadcasting experiment complete message..."
scriptController.update("MyExperiment Script",
"Experiment Complete!")
def __init__(self, name, lutObj='energytable', objType=0, rootNameSpace={}):
'''Constructor - Only succeed if it find the lookup table, otherwise raise exception.'''
self.finder=Finder.getInstance()
self.lut=self.finder.find(lutObj)
if self.lut==None:
raise Exception, "Can not find the Lookup Table object"
self.rootNameSpace=rootNameSpace
self.scannableNames=self.lut.getScannableNames()
self._busy=0
self.scannables=[self.rootNameSpace[x] for x in self.scannableNames]
self.setName(name)
self.setLevel(3)
self.objType=objType
self.inputNames=['energy']
def jobs():
"""
Print a string showing the threads running in the command server.
Only shows the live threads.
"""
command_server = Finder.getInstance().find(Jython.SERVER_NAME)
logger.debug("jobs() called")
s = "%-10s %-12s %-8s %-11s %s\n" % ('DATE', 'TIME', 'TYPE', 'INTERRUPTED', 'COMMAND')
thread_infos = command_server.getCommandThreadInfo()
for t in thread_infos:
date = t.getDate()
time = t.getTime()
thread_type = t.getCommandThreadType()
cmd = t.getCommand();
intrpt = ' X ' if t.isInterrupted() else ''
s += "%(date)-10s %(time)-12s %(thread_type)-8s %(intrpt)-11s %(cmd)s\n" % locals()
print s
def jobs():
"""
Print a string showing the threads running in the command server.
Only shows the live threads.
"""
command_server = Finder.getInstance().find(Jython.SERVER_NAME)
logger.debug("jobs() called")
s = "%-10s %-12s %-8s %-11s %s\n" % ('DATE', 'TIME', 'TYPE', 'INTERRUPTED',
'COMMAND')
thread_infos = command_server.getCommandThreadInfo()
for t in thread_infos:
date = t.getDate()
time = t.getTime()
thread_type = t.getCommandThreadType()
cmd = t.getCommand()
intrpt = ' X ' if t.isInterrupted() else ''
s += "%(date)-10s %(time)-12s %(thread_type)-8s %(intrpt)-11s %(cmd)s\n" % locals(
)
print s
def reload_tables(logInfo=True):
"""reloads all lookup tables on the ObjectServer"""
ok = True
controller = None
prefix = "reload_tables:"
if( logInfo ):
handle_messages.log(controller, prefix + " - started")
finder = Finder.getInstance()
converters = finder.listAllObjects("IReloadableQuantitiesConverter")
for converter in converters:
try:
if( logInfo ):
handle_messages.log(controller, prefix + "..." + converter.getName() )
converter.reloadConverter()
except:
type1, exception, traceback = sys.exc_info()
handle_messages.log(controller, prefix + " - ", type1, exception, traceback, False)
ok = False
if( logInfo ):
handle_messages.log(controller, prefix + " - completed")
if( not ok):
print "reload_tables completed with error"
return ok
def meta_clear_alldynamical():
metashop = Finder.getInstance().find("metashop")
if metashop is None:
return
metashop.clearDynamicScannableMetadata()
return metashop.list(False)
def ls(self):
metascannables = Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
# meta_ls and meta_ll enforce their own formatting, so return their
# list of metadata scannables in our format.
return ' '.join([scn.name for scn in metascannables])
def testMCA():
beamline = Finder.getInstance().find("Beamline")
return plotY(
"Point", "Counts",
beamline.getValue(ReturnType.DBR_NATIVE, "", "-EA-DET-01:MCA-01:mca3"))
ANY CHANGES WILL BE OVERWRITTEN WITHOUT WARNING
'''
# generation-time attributes
__beamline__ = 'EXAMPLE'
__gdaversion__ = '9.9.0pre'
__xmlfile__ = '/home/pi/server_20180710-1656_linux64/rpi-config/rpi-config/servers/main/dummy/server.xml'
__pid__ = '803'
__hostname__ = 'raspberrypi'
__timestamp__ = '2018-09-13 09:05:15.862'
# get function (finder.find for now)
from gda.factory import Finder
get = Finder.getInstance().find
del Finder
# not executed so types not in: dir(gdaserver)
if False:
# fake imports for fake assignments below
from gda.data import ObservablePathConstructor
from gda.data.metadata import GdaMetadata
from gda.data.metadata import NXMetaDataProvider
from gda.device.detector import DummyMandelbrotMappingDetector
from gda.device.detector import NXDetector
from gda.device.motor import DummyMotor
from gda.device.scannable import ScannableMotor
from gda.device.scannable import TwoJawSlitGap
from gda.device.scannable import TwoJawSlitPosition
def meta_clear_alldynamical():
metashop = Finder.getInstance().find("metashop")
if metashop is None:
return
metashop.clearDynamicScannableMetadata()
return metashop.list(False)
def _meta_ll():
"""
Command to list the items to be put into the scan metadata. The value of the items will also be listed
"""
metashop=Finder.getInstance().find("metashop")
return metashop.list(True)
def setTitle(title):
"""
Command to set the title that is recorded in the scan file
"""
Finder.getInstance().find("GDAMetadata").setMetadataValue("title", title)
def __init__(self, finder=None):
if finder == None:
finder = Finder.getInstance()
self.reload(finder)
"""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 _meta_ls():
"""
Command to list the items to be put into the scan metadata.
"""
metashop = Finder.getInstance().find("metashop")
return metashop.list(False)
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 ls(self):
metascannables = Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
# meta_ls and meta_ll enforce their own formatting, so return their
# list of metadata scannables in our format.
return ' '.join([scn.name for scn in metascannables])
def _meta_ls():
"""
Command to list the items to be put into the scan metadata.
"""
metashop=Finder.getInstance().find("metashop")
return metashop.list(False)
def getMeta(self):
return Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
def getMeta(self):
return Finder.getInstance().find("metashop").getMetaScannables() \
if self.readFromNexus else self.scannables_to_read
def getTitle():
"""
Command to get the title that is recorded in the scan file
"""
return Finder.getInstance().find("GDAMetadata").getMetadataValue("title")
from gda.data import PathConstructor
from gda.factory import Finder
import sys
import gda.device.scannable.DummyScannable
from gda.configuration.properties import LocalProperties
import subprocess
from gda.device import Scannable
from gda.jython.commands.GeneralCommands import ls_names, vararg_alias
from time import sleep
from gda.jython.commands import GeneralCommands
from gda.epics import CAClient
from epics_scripts.pv_scannable_utils import caputStringAsWaveform
# set up a nice method for getting the latest file path
i11NumTracker = NumTracker("i11");
finder = Finder.getInstance()
ca=CAClient()
def wd():
dir = PathConstructor.createFromDefaultProperty()
return dir
# function to find the last file path
def pwd():
dir = PathConstructor.createFromDefaultProperty()
filenumber = i11NumTracker.getCurrentFileNumber();
return os.path.join(dir, str(filenumber))
def __init__(self):
resistrarDict = Finder.getInstance().getFindablesOfType(IFileRegistrar)
self.registrars = resistrarDict.values()
def getTitle():
"""
Command to get the title that is recorded in the scan file
"""
return Finder.getInstance().find("GDAMetadata").getMetadataValue("title")
"""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"""
def _meta_ll():
"""
Command to list the items to be put into the scan metadata. The value of the items will also be listed
"""
metashop = Finder.getInstance().find("metashop")
return metashop.list(True)
def testMCA():
beamline = Finder.getInstance().find("Beamline")
return plotY("Point","Counts",beamline.getValue(ReturnType.DBR_NATIVE,"","-EA-DET-01:MCA-01:mca3"))
def setTitle(title):
"""
Command to set the title that is recorded in the scan file
"""
Finder.getInstance().find("GDAMetadata").setMetadataValue("title", title)
def __init__(self, name):
self.tfg = Finder.getInstance().find("tfg")
self.daserver = Finder.getInstance().find("daserver")
# to support showArmed status
self.tfg.setShowArmed(True)
'''
Created on 10 Oct 2014
@author: fy65
'''
from gda.device import Detector
from gda.device.scannable import DummyScannable
from gda.factory import Finder
from gda.jython.commands.ScannableCommands import scan
ds1=DummyScannable("ds1")
NDR=0
CAL=1
calName=Finder.getInstance().find("calibrantName")
dr=Finder.getInstance().find("datareduction")
def ldescan(*args):
MUSTADDDATAREDUCTIONATEND=False
newargs=[]
i=0
#processing 1st argument
if (args[i] == NDR):
i=1
if (isinstance(args[i], Detector)) :
newargs.append(ds1) # @UndefinedVariable
newargs.append(1.0)
newargs.append(1.0)
newargs.append(1.0)
while i<len(args):
newargs.append(args[i])
i=i+1