def getDataCollectionGroupId(self, _dataCollectionId):
self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
dataCollectionGroupId = None
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(_dataCollectionId)
edPluginISPyBRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
if xsDataResultRetrieveDataCollection is not None:
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
if dataCollection is not None:
dataCollectionGroupId = dataCollection.dataCollectionGroupId
self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
return dataCollectionGroupId
def getDataCollectionGroupId(self, _dataCollectionId):
self.DEBUG("EDPluginControlInterfacev1_2.getDataCollectionGroupId")
self.DEBUG("dataCollectionId = {0}".format(_dataCollectionId))
dataCollectionGroupId = None
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = XSDataInteger(_dataCollectionId)
edPluginISPyBRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
if xsDataResultRetrieveDataCollection is not None:
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
if dataCollection is not None:
dataCollectionGroupId = dataCollection.dataCollectionGroupId
self.DEBUG("dataCollectionGroupId = {0}".format(dataCollectionGroupId))
return dataCollectionGroupId
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlXia2DIALSv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
imageNoStart = ispybDataCollection.startImageNumber
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.value
template = self.dataInput.templateN.value
imageNoStart = self.dataInput.fromN.value
imageNoEnd = self.dataInput.toN.value
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0755)
# Create path to pyarch
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(self.resultsDirectory)
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if self.pyarchDirectory is not None and not os.path.exists(self.pyarchDirectory):
os.makedirs(self.pyarchDirectory, 0755)
# Determine pyarch prefix
listPrefix = template.split("_")
self.pyarchPrefix = "di_{0}_run{1}".format(listPrefix[-3], listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage for beamline in ["id23eh1", "id29"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
# Prepare input to execution plugin
xsDataInputXia2DIALSAnom = XSDataInputXia2DIALS()
xsDataInputXia2DIALSAnom.anomalous = XSDataBoolean(True)
if self.doAnomAndNonanom:
xsDataInputXia2DIALSNoanom = XSDataInputXia2DIALS()
xsDataInputXia2DIALSNoanom.anomalous = XSDataBoolean(False)
if isH5:
masterFilePath = os.path.join(directory,
self.eiger_template_to_master(template))
xsDataInputXia2DIALSAnom.addImage(XSDataFile(XSDataString(masterFilePath)))
if self.doAnomAndNonanom:
xsDataInputXia2DIALSNoanom.addImage(XSDataFile(XSDataString(masterFilePath)))
else:
xsDataInputXia2DIALSAnom.addImage(XSDataFile(XSDataString(pathToStartImage)))
if self.doAnomAndNonanom:
xsDataInputXia2DIALSNoanom.addImage(XSDataFile(XSDataString(pathToStartImage)))
timeStart = time.localtime()
self.edPluginExecXia2DIALSAnom.dataInput = xsDataInputXia2DIALSAnom
self.edPluginExecXia2DIALSAnom.execute()
if self.doAnomAndNonanom:
self.edPluginExecXia2DIALSNoanom.dataInput = xsDataInputXia2DIALSNoanom
self.edPluginExecXia2DIALSNoanom.execute()
self.edPluginExecXia2DIALSAnom.synchronize()
if self.doAnomAndNonanom:
self.edPluginExecXia2DIALSNoanom.synchronize()
timeEnd = time.localtime()
# Upload to ISPyB
self.uploadToISPyB(self.edPluginExecXia2DIALSAnom, True, proposal, timeStart, timeEnd)
if self.doAnomAndNonanom:
self.uploadToISPyB(self.edPluginExecXia2DIALSNoanom, False, proposal, timeStart, timeEnd)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlCrystFELv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
userName = os.environ["USER"]
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
#self.messenger.sendProcessingStatus(self.dataInput.dataCollectionId.value,
# "CrystFEL",
# "started")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.ispyb_retrieve_dc_plugin.dataInput = xsDataInputRetrieveDataCollection
self.ispyb_retrieve_dc_plugin.executeSynchronous()
ispybDataCollection = self.ispyb_retrieve_dc_plugin.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
if EDUtilsPath.isEMBL():
#TODO PE2 has 7 digits others 5
template = ispybDataCollection.fileTemplate.replace(
"%07d", "####")
else:
template = ispybDataCollection.fileTemplate.replace(
"%04d", "####")
imageNoStart = ispybDataCollection.startImageNumber
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
dir_parts = processDirectory.split("/")
processDirectory = "/data/users/%s" % os.path.join(*dir_parts[5:])
# Make results directory
self.resultsDirectory = os.path.join(processDirectory,
"crystfel_results")
try:
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory)
except Exception as ex:
print ex
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
directory)
#TODO: enable when ready
"""
if self.pyarchDirectory is not None:
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if not os.path.exists(self.pyarchDirectory):
os.makedirs(self.pyarchDirectory)
"""
self.baseFileName = "%s/crystfel_xgandalf_%d" % (
self.resultsDirectory, self.dataInput.dataCollectionId.value)
xsDataInputCrystFEL = XSDataInputCrystFEL()
# Check if imagesFullPath exists. If not then generate one
if self.dataInput.imagesFullPath is None:
imagesFullPath = "%s_images_fullpath.lst" % self.baseName
imagesFullFile = open(imagesFullPath, "w")
for index in range(imageNoEnd - imageNoStart + 1):
imagePath = os.path.join(
directory, ispybDataCollection.fileTemplate % (index + 1))
imagesFullFile.write("%s\n" % imagePath)
imagesFullFile.close()
xsDataInputCrystFEL.imagesFullPath = XSDataString(imagesFullPath)
else:
xsDataInputCrystFEL.imagesFullPath = self.dataInput.imagesFullPath
xsDataInputCrystFEL.geomFile = self.dataInput.geomFile
xsDataInputCrystFEL.cellFile = self.dataInput.cellFile
xsDataInputCrystFEL.pointGroup = self.dataInput.pointGroup
xsDataInputCrystFEL.spaceGroup = self.dataInput.spaceGroup
xsDataInputCrystFEL.resCutOff = self.dataInput.resCutOff
xsDataInputCrystFEL.baseFileName = XSDataString(self.baseFileName)
self.timeStart = time.localtime()
self.integration_id, self.program_id = self.create_integration_id(
self.dataInput.dataCollectionId.value, "Creating integration ID")
self.index_plugin.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin_odd.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin_even.dataInput = xsDataInputCrystFEL
self.partialator_plugin.dataInput = xsDataInputCrystFEL
self.post_process_plugin.dataInput = xsDataInputCrystFEL
self.post_process_plugin.dataOutput = XSDataResultCrystFEL
self.process_hkl_plugin_odd.process_hkl_options += " --odd-only"
self.process_hkl_plugin_odd.process_hkl_type = "o"
self.process_hkl_plugin_even.process_hkl_options += " --even-only"
self.process_hkl_plugin_even.process_hkl_type = "e"
self.index_plugin.executeSynchronous()
if self.index_plugin.isFailure():
self.ERROR('indexamajig: Failed')
self.setFailure()
return
else:
self.screen('indexamajig: Finished')
self.process_hkl_plugin.executeSynchronous()
if self.process_hkl_plugin.isFailure():
self.ERROR('process_hkl: Failed')
self.setFailure()
return
else:
self.screen('process_hkl: Finished')
self.process_hkl_plugin_odd.executeSynchronous()
if self.process_hkl_plugin_odd.isFailure():
self.ERROR('process_hkl_odd: Failed')
self.setFailure()
return
else:
self.screen('process_hkl_odd: Finished')
self.process_hkl_plugin_even.executeSynchronous()
if self.process_hkl_plugin_even.isFailure():
self.ERROR('process_hkl_even: Failed')
self.setFailure()
return
else:
self.screen('process_hkl_even: Finished')
self.partialator_plugin.executeSynchronous()
if self.partialator_plugin.isFailure():
self.ERROR('partialator: Failed')
self.setFailure()
return
else:
self.screen('partialator: Finished')
self.post_process_plugin.executeSynchronous()
if self.post_process_plugin.isFailure():
self.ERROR('post_process: Failed')
self.setFailure()
return
else:
self.screen('post_process: Finished')
self.timeEnd = time.localtime()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlXDSAPPv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
if self.dataInput.startImageNumber is not None:
imageNoStart = self.dataInput.startImageNumber.value
if self.dataInput.endImageNumber is not None:
imageNoEnd = self.dataInput.endImageNumber.value
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
if imageNoStart is None:
imageNoStart = ispybDataCollection.startImageNumber
if imageNoEnd is None:
imageNoEnd = ispybDataCollection.startImageNumber + \
ispybDataCollection.numberOfImages - 1
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.value
template = self.dataInput.templateN.value
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
# Create path to pyarch
if self.dataInput.reprocess is not None and self.dataInput.reprocess.value:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchReprocessDirectoryPath(beamline,
"XDSAPP", self.dataInput.dataCollectionId.value)
else:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(self.resultsDirectory)
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if self.pyarchDirectory is not None and not os.path.exists(self.pyarchDirectory):
try:
os.makedirs(self.pyarchDirectory, 0o755)
except:
self.pyarchDirectory = None
# Determine pyarch prefix
listPrefix = template.split("_")
self.pyarchPrefix = "xa_{0}_run{1}".format(listPrefix[-3], listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage for beamline in ["id30b"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id23eh1", "id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
if self.dataInput.hdf5ToCbfDirectory is not None:
dir = self.dataInput.hdf5ToCbfDirectory.path.value
pathToStartImage = glob.glob(os.path.join(dir, "*000001*"))[0]
self.timeStart = time.localtime()
# Prepare input to execution plugin
if self.doAnom:
xsDataInputXDSAPPAnom = XSDataInputXDSAPP()
xsDataInputXDSAPPAnom.startImageNumber = self.dataInput.startImageNumber
xsDataInputXDSAPPAnom.endImageNumber = self.dataInput.endImageNumber
xsDataInputXDSAPPAnom.anomalous = XSDataBoolean(True)
xsDataInputXDSAPPAnom.image = XSDataFile(XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPAnom.spacegroup = XSDataString(self.xdsAppSpacegroup)
self.edPluginExecXDSAPPAnom.dataInput = xsDataInputXDSAPPAnom
self.edPluginExecXDSAPPAnom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=True,
timeStart=self.timeStart)
if self.doNoanom:
xsDataInputXDSAPPNoanom = XSDataInputXDSAPP()
xsDataInputXDSAPPNoanom.startImageNumber = self.dataInput.startImageNumber
xsDataInputXDSAPPNoanom.endImageNumber = self.dataInput.endImageNumber
xsDataInputXDSAPPNoanom.anomalous = XSDataBoolean(False)
xsDataInputXDSAPPNoanom.image = XSDataFile(XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPNoanom.spacegroup = XSDataString(self.xdsAppSpacegroup)
self.edPluginExecXDSAPPNoanom.dataInput = xsDataInputXDSAPPNoanom
self.edPluginExecXDSAPPNoanom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=False,
timeStart=self.timeStart)
if self.doAnom:
self.edPluginExecXDSAPPAnom.synchronize()
xsDataResultXDSAPPAnom = self.edPluginExecXDSAPPAnom.dataOutput
# Run XSCALE even if XSCALE.LP is present
strPathXscaleLpAnom = self.runXscale(self.edPluginExecXDSAPPAnom.getWorkingDirectory(), anom=True, merged=True)
if self.doNoanom:
self.edPluginExecXDSAPPNoanom.synchronize()
xsDataResultXDSAPPNoanom = self.edPluginExecXDSAPPNoanom.dataOutput
strPathXscaleLpNoanom = self.runXscale(self.edPluginExecXDSAPPNoanom.getWorkingDirectory(), anom=False, merged=True)
self.timeEnd = time.localtime()
# Upload to ISPyB
if self.dataInput.dataCollectionId is not None:
# Check if we should use XDS_ASCII_to_XML.pl
if self.doAnom:
if self.useXdsAsciiToXml:
# Only for anom runs
self.runXdsAsciiToXml(xsDataResultXDSAPPAnom,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom)
else:
self.hasUploadedAnomResultsToISPyB = self.uploadToISPyB(xsDataResultXDSAPPAnom, processDirectory, template,
strPathXscaleLpAnom, True, proposal, self.timeStart, self.timeEnd,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom)
if self.hasUploadedAnomResultsToISPyB:
self.screen("Anom results uploaded to ISPyB")
else:
self.ERROR("Could not upload anom results to ISPyB!")
if self.doNoanom:
self.hasUploadedNoanomResultsToISPyB = self.uploadToISPyB(xsDataResultXDSAPPNoanom, processDirectory, template,
strPathXscaleLpNoanom, False, proposal, self.timeStart, self.timeEnd,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom)
if self.hasUploadedNoanomResultsToISPyB:
self.screen("Noanom results uploaded to ISPyB")
else:
self.ERROR("Could not upload noanom results to ISPyB!")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlXia2DIALSv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
if EDUtilsPath.isEMBL():
template = ispybDataCollection.fileTemplate.replace(
"%05d", "####")
else:
template = ispybDataCollection.fileTemplate.replace(
"%04d", "####")
if self.dataInput.startFrame is None:
imageNoStart = ispybDataCollection.startImageNumber
else:
imageNoStart = self.dataInput.startFrame.value
if self.dataInput.endFrame is None:
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
else:
imageNoEnd = self.dataInput.endFrame.value
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(
directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(
directory, ispybDataCollection.fileTemplate % imageNoEnd)
# else:
# directory = self.dataInput.dirN.value
# template = self.dataInput.templateN.value
# imageNoStart = self.dataInput.fromN.value
# imageNoEnd = self.dataInput.toN.value
# fileTemplate = template.replace("####", "%04d")
# pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
# pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
# Create path to pyarch
if self.dataInput.reprocess is not None and self.dataInput.reprocess.value:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchReprocessDirectoryPath(
beamline, "XIA2_DIALS", self.dataInput.dataCollectionId.value)
else:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
self.resultsDirectory)
if self.pyarchDirectory is not None:
self.pyarchDirectory = self.pyarchDirectory.replace(
'PROCESSED_DATA', 'RAW_DATA')
if not os.path.exists(self.pyarchDirectory):
try:
os.makedirs(self.pyarchDirectory, 0o755)
except:
self.pyarchDirectory = None
# Determine pyarch prefix
listPrefix = template.split("_")
self.pyarchPrefix = "di_{0}_run{1}".format(listPrefix[-3],
listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage
for beamline in ["id23eh1", "id29"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage
for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(
directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(
directory, self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
if EDUtilsPath.isEMBL():
fWaitFileTimeout = 60
else:
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(
XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (
fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(
XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (
fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
# Prepare input to execution plugin
if self.doAnom:
xsDataInputXia2DIALSAnom = XSDataInputXia2DIALS()
xsDataInputXia2DIALSAnom.anomalous = XSDataBoolean(True)
xsDataInputXia2DIALSAnom.spaceGroup = self.dataInput.spaceGroup
xsDataInputXia2DIALSAnom.unitCell = self.dataInput.unitCell
if imageNoStart is not None:
xsDataInputXia2DIALSAnom.startFrame = XSDataInteger(
imageNoStart)
if imageNoEnd is not None:
xsDataInputXia2DIALSAnom.endFrame = XSDataInteger(imageNoEnd)
if self.doNoanom:
xsDataInputXia2DIALSNoanom = XSDataInputXia2DIALS()
xsDataInputXia2DIALSNoanom.anomalous = XSDataBoolean(False)
xsDataInputXia2DIALSNoanom.spaceGroup = self.dataInput.spaceGroup
xsDataInputXia2DIALSNoanom.unitCell = self.dataInput.unitCell
if imageNoStart is not None:
xsDataInputXia2DIALSNoanom.startFrame = XSDataInteger(
imageNoStart)
if imageNoEnd is not None:
xsDataInputXia2DIALSNoanom.endFrame = XSDataInteger(imageNoEnd)
if isH5:
masterFilePath = os.path.join(
directory, self.eiger_template_to_master(template))
if self.doAnom:
xsDataInputXia2DIALSAnom.addImage(
XSDataFile(XSDataString(masterFilePath)))
if self.doNoanom:
xsDataInputXia2DIALSNoanom.addImage(
XSDataFile(XSDataString(masterFilePath)))
else:
if self.doAnom:
xsDataInputXia2DIALSAnom.addImage(
XSDataFile(XSDataString(pathToStartImage)))
if self.doNoanom:
xsDataInputXia2DIALSNoanom.addImage(
XSDataFile(XSDataString(pathToStartImage)))
self.timeStart = time.localtime()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to running
if self.doAnom:
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingPrograms,
isAnom=True,
timeStart=self.timeStart)
if self.doNoanom:
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingPrograms,
isAnom=False,
timeStart=self.timeStart)
if self.doAnom:
self.edPluginExecXia2DIALSAnom.dataInput = xsDataInputXia2DIALSAnom
self.edPluginExecXia2DIALSAnom.execute()
if self.doNoanom:
self.edPluginExecXia2DIALSNoanom.dataInput = xsDataInputXia2DIALSNoanom
self.edPluginExecXia2DIALSNoanom.execute()
if self.doAnom:
self.edPluginExecXia2DIALSAnom.synchronize()
if self.doNoanom:
self.edPluginExecXia2DIALSNoanom.synchronize()
self.timeEnd = time.localtime()
# Upload to ISPyB
if self.doAnom:
self.hasUploadedAnomResultsToISPyB = self.uploadToISPyB(
self.edPluginExecXia2DIALSAnom, True, proposal,
self.autoProcProgramIdAnom, self.autoProcIntegrationIdAnom)
if self.hasUploadedAnomResultsToISPyB:
self.screen("Anom results uploaded to ISPyB")
else:
self.ERROR("Could not upload anom results to ISPyB!")
if self.doNoanom:
self.hasUploadedNoanomResultsToISPyB = self.uploadToISPyB(
self.edPluginExecXia2DIALSNoanom, False, proposal,
self.autoProcProgramIdNoanom, self.autoProcIntegrationIdNoanom)
if self.hasUploadedNoanomResultsToISPyB:
self.screen("Noanom results uploaded to ISPyB")
else:
self.ERROR("Could not upload noanom results to ISPyB!")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlXDSAPPv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
imageNoStart = ispybDataCollection.startImageNumber
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.value
template = self.dataInput.templateN.value
imageNoStart = self.dataInput.fromN.value
imageNoEnd = self.dataInput.toN.value
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
isH5 = False
if any(beamline in pathToStartImage for beamline in ["id23eh1", "id29"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
if self.dataInput.hdf5ToCbfDirectory is not None:
dir = self.dataInput.hdf5ToCbfDirectory.path.value
pathToStartImage = glob.glob(os.path.join(dir, "*000001*"))[0]
# Prepare input to execution plugin
xsDataInputXDSAPPAnom = XSDataInputXDSAPP()
xsDataInputXDSAPPAnom.anomalous = XSDataBoolean(True)
xsDataInputXDSAPPAnom.image = XSDataFile(XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPAnom.spacegroup = XSDataString(self.xdsAppSpacegroup)
if self.doAnomAndNonanom:
xsDataInputXDSAPPNoanom = XSDataInputXDSAPP()
xsDataInputXDSAPPNoanom.anomalous = XSDataBoolean(False)
xsDataInputXDSAPPNoanom.image = XSDataFile(XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPNoanom.spacegroup = XSDataString(self.xdsAppSpacegroup)
# if isH5:
# masterFilePath = os.path.join(directory,
# self.eiger_template_to_master(template))
# xsDataInputXDSAPPAnom.addImage(XSDataFile(XSDataString(masterFilePath)))
# if self.doAnomAndNonanom:
# xsDataInputXDSAPPNoanom.addImage(XSDataFile(XSDataString(masterFilePath)))
# else:
# xsDataInputXDSAPPAnom.addImage(XSDataFile(XSDataString(pathToStartImage)))
# if self.doAnomAndNonanom:
# xsDataInputXDSAPPNoanom.addImage(XSDataFile(XSDataString(pathToStartImage)))
self.timeStart = time.localtime()
self.edPluginExecXDSAPPAnom.dataInput = xsDataInputXDSAPPAnom
self.edPluginExecXDSAPPAnom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=True,
timeStart=self.timeStart)
if self.doAnomAndNonanom:
self.edPluginExecXDSAPPNoanom.dataInput = xsDataInputXDSAPPNoanom
self.edPluginExecXDSAPPNoanom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=False,
timeStart=self.timeStart)
self.edPluginExecXDSAPPAnom.synchronize()
xsDataResultXDSAPPAnom = self.edPluginExecXDSAPPAnom.dataOutput
# Run XSCALE even if XSCALE.LP is present
strPathXscaleLpAnom = self.runXscale(self.edPluginExecXDSAPPAnom.getWorkingDirectory(), anom=True, merged=True)
if self.doAnomAndNonanom:
self.edPluginExecXDSAPPNoanom.synchronize()
xsDataResultXDSAPPNoanom = self.edPluginExecXDSAPPNoanom.dataOutput
strPathXscaleLpNoanom = self.runXscale(self.edPluginExecXDSAPPNoanom.getWorkingDirectory(), anom=False, merged=True)
self.timeEnd = time.localtime()
# Upload to ISPyB
if self.dataInput.dataCollectionId is not None:
# Check if we should use XDS_ASCII_to_XML.pl
if self.useXdsAsciiToXml:
# Only for anom runs
self.runXdsAsciiToXml(xsDataResultXDSAPPAnom,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom)
else:
self.hasUploadedAnomResultsToISPyB = self.uploadToISPyB(xsDataResultXDSAPPAnom, processDirectory, template,
strPathXscaleLpAnom, True, proposal, self.timeStart, self.timeEnd,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom)
if self.hasUploadedAnomResultsToISPyB:
self.screen("Anom results uploaded to ISPyB")
else:
self.ERROR("Could not upload anom results to ISPyB!")
if self.doAnomAndNonanom:
self.hasUploadedNoanomResultsToISPyB = self.uploadToISPyB(xsDataResultXDSAPPNoanom, processDirectory, template,
strPathXscaleLpNoanom, False, proposal, self.timeStart, self.timeEnd,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom)
if self.hasUploadedNoanomResultsToISPyB:
self.screen("Noanom results uploaded to ISPyB")
else:
self.ERROR("Could not upload noanom results to ISPyB!")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_0.process")
self.sendMessageToMXCuBE("Processing started...", "info")
EDUtilsParallel.initializeNbThread()
xsDataResultControlDozor = XSDataResultControlDozor()
# Check if connection to ISPyB needed
if self.dataInput.dataCollectionId is not None:
edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = edPluginRetrieveDataCollection.dataOutput.dataCollection
if self.batchSize is None:
batchSize = ispybDataCollection.numberOfImages
else:
batchSize = self.batchSize
if batchSize > self.maxBatchSize:
batchSize = self.maxBatchSize
if abs(ispybDataCollection.overlap) > 1:
self.hasOverlap = True
self.overlap = ispybDataCollection.overlap
dictImage = self.createImageDictFromISPyB(ispybDataCollection)
else:
# No connection to ISPyB, take parameters from input
if self.dataInput.batchSize is None:
batchSize = self.maxBatchSize
else:
batchSize = self.dataInput.batchSize.value
dictImage = self.createImageDict(self.dataInput)
self.screen("Dozor batch size: {0}".format(batchSize))
if self.dataInput.hdf5BatchSize is not None:
self.hdf5BatchSize = self.dataInput.hdf5BatchSize.value
listAllBatches = self.createListOfBatches(dictImage.keys(), batchSize)
if dictImage[listAllBatches[0][0]].path.value.endswith("h5"):
# Convert HDF5 images to CBF
self.screen("HDF5 converter batch size: {0}".format(self.batchSize))
if self.doRadiationDamage:
self.cbfTempDir = None
else:
self.cbfTempDir = tempfile.mkdtemp(prefix="CbfTemp_")
listHdf5Batches = self.createListOfBatches(dictImage.keys(), self.batchSize)
dictImage, self.hasHdf5Prefix = self.convertToCBF(dictImage, listHdf5Batches, self.doRadiationDamage)
for listBatch in listAllBatches:
# Read the header from the first image in the batch
xsDataFile = dictImage[listBatch[0]]
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataInteger(3)
xsDataInputDozor.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputDozor.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
xsDataInputDozor.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputDozor.imageStep : XSDataDouble optional
xsDataInputDozor.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputDozor.firstImageNumber = subWedge.image[0].number
xsDataInputDozor.numberImages = XSDataInteger(len(listBatch))
if self.hasOverlap:
xsDataInputDozor.overlap = XSDataAngle(self.overlap)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
if EDUtilsPath.isEMBL():
strXDSTemplate = "%s_?????.%s" % (strPrefix, strSuffix)
elif self.hasHdf5Prefix and not self.hasOverlap:
strXDSTemplate = "%s_??????.%s" % (strPrefix, strSuffix)
else:
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputDozor.nameTemplateImage = XSDataString(os.path.join(os.path.dirname(strFileName), strXDSTemplate))
xsDataInputDozor.wedgeNumber = self.dataInput.wedgeNumber
xsDataInputDozor.radiationDamage = self.dataInput.radiationDamage
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor_%05d" % subWedge.image[0].number.value)
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.execute()
edPluginDozor.synchronize()
indexImage = 0
imageDozorBatchList = []
for xsDataResultDozor in edPluginDozor.dataOutput.imageDozor:
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.number = xsDataResultDozor.number
xsDataControlImageDozor.image = dictImage[listBatch[indexImage]]
xsDataControlImageDozor.spotsNumOf = xsDataResultDozor.spotsNumOf
xsDataControlImageDozor.spotsIntAver = xsDataResultDozor.spotsIntAver
xsDataControlImageDozor.spotsResolution = xsDataResultDozor.spotsResolution
xsDataControlImageDozor.powderWilsonScale = xsDataResultDozor.powderWilsonScale
xsDataControlImageDozor.powderWilsonBfactor = xsDataResultDozor.powderWilsonBfactor
xsDataControlImageDozor.powderWilsonResolution = xsDataResultDozor.powderWilsonResolution
xsDataControlImageDozor.powderWilsonCorrelation = xsDataResultDozor.powderWilsonCorrelation
xsDataControlImageDozor.powderWilsonRfactor = xsDataResultDozor.powderWilsonRfactor
xsDataControlImageDozor.mainScore = xsDataResultDozor.mainScore
xsDataControlImageDozor.spotScore = xsDataResultDozor.spotScore
xsDataControlImageDozor.visibleResolution = xsDataResultDozor.visibleResolution
xsDataControlImageDozor.spotFile = xsDataResultDozor.spotFile
xsDataControlImageDozor.angle = xsDataResultDozor.angle
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
if xsDataResultControlDozor.inputDozor is None:
xsDataResultControlDozor.inputDozor = XSDataDozorInput().parseString(xsDataInputDozor.marshal())
indexImage += 1
dozorSpotListShape = []
dozorSpotList = []
spotFile = None
if xsDataControlImageDozor.spotFile is not None:
spotFile = xsDataControlImageDozor.spotFile.path.value
if os.path.exists(spotFile):
numpyArray = numpy.loadtxt(spotFile, skiprows=3)
dozorSpotList = base64.b64encode(numpyArray.tostring())
dozorSpotListShape.append(numpyArray.shape[0])
if len(numpyArray.shape) > 1:
dozorSpotListShape.append(numpyArray.shape[1])
imageDozorDict = {"index": xsDataControlImageDozor.number.value,
"imageName": xsDataControlImageDozor.image.path.value,
"dozor_score": xsDataControlImageDozor.mainScore.value,
"dozorSpotsNumOf" : xsDataControlImageDozor.spotsNumOf.value,
"dozorSpotFile": spotFile,
"dozorSpotList" : dozorSpotList,
"dozorSpotListShape": dozorSpotListShape,
"dozorSpotsIntAver": xsDataControlImageDozor.spotsIntAver.value,
"dozorSpotsResolution": xsDataControlImageDozor.spotsResolution.value
}
imageDozorBatchList.append(imageDozorDict)
xsDataResultControlDozor.halfDoseTime = edPluginDozor.dataOutput.halfDoseTime
xsDataResultControlDozor.pngPlots = edPluginDozor.dataOutput.pngPlots
self.sendResultToMXCuBE(imageDozorBatchList)
self.sendMessageToMXCuBE("Batch processed")
self.dataOutput = xsDataResultControlDozor
if self.cbfTempDir is not None:
if self.dataInput.keepCbfTmpDirectory is not None and self.dataInput.keepCbfTmpDirectory.value:
self.dataOutput.pathToCbfDirectory = XSDataFile(XSDataString(self.cbfTempDir))
else:
shutil.rmtree(self.cbfTempDir)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_0.process")
xsDataResultControlDozor = XSDataResultControlDozor()
# Check if connection to ISPyB needed
if self.dataInput.dataCollectionId is not None:
edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = edPluginRetrieveDataCollection.dataOutput.dataCollection
batchSize = ispybDataCollection.numberOfImages
if batchSize > self.maxBatchSize:
batchSize = self.maxBatchSize
if abs(ispybDataCollection.overlap) > 1:
self.hasOverlap = True
self.overlap = ispybDataCollection.overlap
dictImage = self.createImageDictFromISPyB(ispybDataCollection)
else:
# No connection to ISPyB, take parameters from input
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
dictImage = self.createImageDict(self.dataInput)
listAllBatches = self.createListOfBatches(dictImage.keys(), batchSize)
if dictImage[listAllBatches[0][0]].path.value.endswith("h5"):
# Convert HDF5 images to CBF
self.cbfTempDir = tempfile.mkdtemp(prefix="CbfTemp_")
dictImage, self.hasHdf5Prefix = self.convertToCBF(dictImage)
for listBatch in listAllBatches:
# Read the header from the first image in the batch
xsDataFile = dictImage[listBatch[0]]
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataInteger(3)
xsDataInputDozor.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputDozor.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
xsDataInputDozor.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputDozor.imageStep : XSDataDouble optional
xsDataInputDozor.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputDozor.firstImageNumber = subWedge.image[0].number
xsDataInputDozor.numberImages = XSDataInteger(len(listBatch))
if self.hasOverlap:
xsDataInputDozor.overlap = XSDataAngle(self.overlap)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
if EDUtilsPath.isEMBL():
strXDSTemplate = "%s_?????.%s" % (strPrefix, strSuffix)
elif self.hasHdf5Prefix and not self.hasOverlap:
strXDSTemplate = "%s_??????.%s" % (strPrefix, strSuffix)
else:
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputDozor.nameTemplateImage = XSDataString(
os.path.join(os.path.dirname(strFileName), strXDSTemplate)
)
xsDataInputDozor.wedgeNumber = self.dataInput.wedgeNumber
xsDataInputDozor.radiationDamage = self.dataInput.radiationDamage
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor_%05d" % subWedge.image[0].number.value)
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.executeSynchronous()
indexImage = 0
for xsDataResultDozor in edPluginDozor.dataOutput.imageDozor:
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.number = xsDataResultDozor.number
xsDataControlImageDozor.image = dictImage[listBatch[indexImage]]
xsDataControlImageDozor.spotsNumOf = xsDataResultDozor.spotsNumOf
xsDataControlImageDozor.spotsIntAver = xsDataResultDozor.spotsIntAver
xsDataControlImageDozor.spotsResolution = xsDataResultDozor.spotsResolution
xsDataControlImageDozor.powderWilsonScale = xsDataResultDozor.powderWilsonScale
xsDataControlImageDozor.powderWilsonBfactor = xsDataResultDozor.powderWilsonBfactor
xsDataControlImageDozor.powderWilsonResolution = xsDataResultDozor.powderWilsonResolution
xsDataControlImageDozor.powderWilsonCorrelation = xsDataResultDozor.powderWilsonCorrelation
xsDataControlImageDozor.powderWilsonRfactor = xsDataResultDozor.powderWilsonRfactor
xsDataControlImageDozor.mainScore = xsDataResultDozor.mainScore
xsDataControlImageDozor.spotScore = xsDataResultDozor.spotScore
xsDataControlImageDozor.visibleResolution = xsDataResultDozor.visibleResolution
xsDataControlImageDozor.spotFile = xsDataResultDozor.spotFile
xsDataControlImageDozor.angle = xsDataResultDozor.angle
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
if xsDataResultControlDozor.inputDozor is None:
xsDataResultControlDozor.inputDozor = XSDataDozorInput().parseString(xsDataInputDozor.marshal())
indexImage += 1
xsDataResultControlDozor.halfDoseTime = edPluginDozor.dataOutput.halfDoseTime
self.dataOutput = xsDataResultControlDozor
if self.cbfTempDir is not None:
shutil.rmtree(self.cbfTempDir)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlAutoPROCv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
if EDUtilsPath.isEMBL():
template = ispybDataCollection.fileTemplate.replace("%05d", "#" * 5)
elif EDUtilsPath.isMAXIV():
template = ispybDataCollection.fileTemplate
else:
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
if self.dataInput.fromN is None:
imageNoStart = ispybDataCollection.startImageNumber
else:
imageNoStart = self.dataInput.fromN.value
if self.dataInput.toN is None:
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
else:
imageNoEnd = self.dataInput.toN.value
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.path.value
template = self.dataInput.templateN.value
imageNoStart = self.dataInput.fromN.value
imageNoEnd = self.dataInput.toN.value
if EDUtilsPath.isEMBL():
fileTemplate = template.replace("#####", "%05d")
else:
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
if EDUtilsPath.isALBA():
_processDirectory = "_".join(pathToStartImage.split('_')[:-1])
from datetime import datetime
_id = datetime.now().strftime('%Y%m%d_%H%M%S')
self.resultsDirectory = os.path.join(_processDirectory, "autoPROC_%s" % _id)
else:
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
# Create path to pyarch
if self.dataInput.reprocess is not None and self.dataInput.reprocess.value:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchReprocessDirectoryPath(beamline,
"autoPROC", self.dataInput.dataCollectionId.value)
else:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(self.resultsDirectory)
if self.pyarchDirectory is not None:
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if not os.path.exists(self.pyarchDirectory):
try:
os.makedirs(self.pyarchDirectory, 0o755)
except:
self.pyarchDirectory = None
# The resultsDirectory is not used at ALBA (only pyarchDirectory)
if EDUtilsPath.isALBA():
self.resultsDirectory = None
# Determine pyarch prefix
if EDUtilsPath.isALBA():
listPrefix = template.split("_")
self.pyarchPrefix = "ap_{0}_{1}".format("_".join(listPrefix[:-2]),
listPrefix[-2])
else:
listPrefix = template.split("_")
self.pyarchPrefix = "ap_{0}_run{1}".format(listPrefix[-3], listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage for beamline in ["id30b"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id23eh1", "id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
if EDUtilsPath.isMAXIV():
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
if EDUtilsPath.isEMBL() or EDUtilsPath.isMAXIV():
fWaitFileTimeout = 60 # s
else:
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
self.timeStart = time.localtime()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to running
if self.doAnom:
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgram,
isAnom=True,
timeStart=self.timeStart)
self.autoProcIntegrationIdAnomStaraniso, self.autoProcProgramIdAnomStaraniso = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgramStaraniso,
isAnom=True,
timeStart=self.timeStart)
if self.doNoanom:
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgram,
isAnom=False,
timeStart=self.timeStart)
self.autoProcIntegrationIdNoanomStaraniso, self.autoProcProgramIdNoanomStaraniso = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgramStaraniso,
isAnom=False,
timeStart=self.timeStart)
# Prepare input to execution plugin
if self.doAnom:
xsDataInputAutoPROCAnom = XSDataInputAutoPROC()
xsDataInputAutoPROCAnom.anomalous = XSDataBoolean(True)
xsDataInputAutoPROCAnom.symm = self.dataInput.symm
xsDataInputAutoPROCAnom.cell = self.dataInput.cell
xsDataInputAutoPROCAnom.lowResolutionLimit = self.dataInput.lowResolutionLimit
xsDataInputAutoPROCAnom.highResolutionLimit = self.dataInput.highResolutionLimit
if self.doNoanom:
xsDataInputAutoPROCNoanom = XSDataInputAutoPROC()
xsDataInputAutoPROCNoanom.anomalous = XSDataBoolean(False)
xsDataInputAutoPROCNoanom.symm = self.dataInput.symm
xsDataInputAutoPROCNoanom.cell = self.dataInput.cell
xsDataInputAutoPROCNoanom.lowResolutionLimit = self.dataInput.lowResolutionLimit
xsDataInputAutoPROCNoanom.highResolutionLimit = self.dataInput.highResolutionLimit
xsDataAutoPROCIdentifier = XSDataAutoPROCIdentifier()
xsDataAutoPROCIdentifier.idN = XSDataString(identifier)
xsDataAutoPROCIdentifier.dirN = XSDataFile(XSDataString(directory))
xsDataAutoPROCIdentifier.templateN = XSDataString(template)
xsDataAutoPROCIdentifier.fromN = XSDataInteger(imageNoStart)
xsDataAutoPROCIdentifier.toN = XSDataInteger(imageNoEnd)
if self.doAnom:
xsDataInputAutoPROCAnom.addIdentifier(xsDataAutoPROCIdentifier)
if self.doNoanom:
xsDataInputAutoPROCNoanom.addIdentifier(xsDataAutoPROCIdentifier.copy())
if isH5:
masterFilePath = os.path.join(directory,
self.eiger_template_to_master(template))
if self.doAnom:
xsDataInputAutoPROCAnom.masterH5 = XSDataFile(XSDataString(masterFilePath))
if self.doNoanom:
xsDataInputAutoPROCNoanom.masterH5 = XSDataFile(XSDataString(masterFilePath))
timeStart = time.localtime()
if self.doAnom:
self.edPluginExecAutoPROCAnom.dataInput = xsDataInputAutoPROCAnom
self.edPluginExecAutoPROCAnom.execute()
if self.doNoanom:
self.edPluginExecAutoPROCNoanom.dataInput = xsDataInputAutoPROCNoanom
self.edPluginExecAutoPROCNoanom.execute()
if self.doAnom:
self.edPluginExecAutoPROCAnom.synchronize()
if self.doNoanom:
self.edPluginExecAutoPROCNoanom.synchronize()
timeEnd = time.localtime()
# Upload to ISPyB
if self.doAnom:
self.uploadToISPyB(self.edPluginExecAutoPROCAnom, True, False, proposal, timeStart, timeEnd)
self.uploadToISPyB(self.edPluginExecAutoPROCAnom, True, True, proposal, timeStart, timeEnd)
if self.doNoanom:
self.uploadToISPyB(self.edPluginExecAutoPROCNoanom, False, False, proposal, timeStart, timeEnd)
self.uploadToISPyB(self.edPluginExecAutoPROCNoanom, False, True, proposal, timeStart, timeEnd)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlCrystFELv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
#self.messenger.sendProcessingStatus(self.dataInput.dataCollectionId.value,
# "CrystFEL",
# "started")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.ispyb_retrieve_dc_plugin.dataInput = xsDataInputRetrieveDataCollection
self.ispyb_retrieve_dc_plugin.executeSynchronous()
ispybDataCollection = self.ispyb_retrieve_dc_plugin.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
if EDUtilsPath.isEMBL():
#TODO PE2 has 7 digits others 5
template = ispybDataCollection.fileTemplate.replace("%07d", "####")
else:
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
imageNoStart = ispybDataCollection.startImageNumber
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
try:
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 755)
except Exception as ex:
print ex
# Create path to pyarch
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(self.resultsDirectory)
#TODO: enable when ready
"""
if self.pyarchDirectory is not None:
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if not os.path.exists(self.pyarchDirectory):
os.makedirs(self.pyarchDirectory, 755)
"""
# Determine pyarch prefix
listPrefix = template.split("_")
self.pyarchPrefix = "di_{0}_run{1}".format(listPrefix[-3], listPrefix[-2])
isH5 = False
minSizeFirst = 1000000
minSizeLast = 1000000
fWaitFileTimeout = 60
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.wait_first_image_plugin.size = XSDataInteger(minSizeFirst)
self.wait_first_image_plugin.dataInput = xsDataInputMXWaitFileFirst
self.wait_first_image_plugin.executeSynchronous()
if self.wait_first_image_plugin.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
self.baseName = "%s/crystfel_xgandalf" % self.resultsDirectory
self.streamFilename = "%s_%d.stream" % (
self.baseName,
self.dataInput.dataCollectionId.value
)
self.hklFilename = "%s_%d.hkl" % (
self.baseName,
self.dataInput.dataCollectionId.value
)
self.mtzFilename = "%s_%d.mtz" % (
self.baseName,
self.dataInput.dataCollectionId.value
)
# Prepare input to execution plugin
xsDataInputCrystFEL = XSDataInputCrystFEL()
# Check if imagesFullPath exists. If not then generate one
if self.dataInput.imagesFullPath is None:
imagesFullPath = "%s_images_fullpath.lst" % self.baseName
imagesFullFile = open(imagesFullPath, "w")
for index in range(imageNoEnd - imageNoStart + 1):
imagePath = os.path.join(directory, ispybDataCollection.fileTemplate % (index + 1))
imagesFullFile.write("%s\n" % imagePath)
imagesFullFile.close()
xsDataInputCrystFEL.imagesFullPath = XSDataString(imagesFullPath)
else:
xsDataInputCrystFEL.imagesFullPath = self.dataInput.imagesFullPath
xsDataInputCrystFEL.geomFile = self.dataInput.geomFile
xsDataInputCrystFEL.cellFile = self.dataInput.cellFile
#TODO EDNA can generate the imagesFull path if id do not exist
xsDataInputCrystFEL.imagesFullPath = self.dataInput.imagesFullPath
xsDataInputCrystFEL.streamFile = XSDataString(self.streamFilename)
xsDataInputCrystFEL.hklFile = XSDataString(self.hklFilename)
xsDataInputCrystFEL.mtzFile = XSDataString(self.mtzFilename)
self.timeStart = time.localtime()
"""
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to running
self.autoProcIntegrationId, self.autoProcProgramId = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingPrograms,
isAnom=True,
timeStart=self.timeStart)
"""
self.index_plugin.dataInput = xsDataInputCrystFEL
self.index_plugin.executeSynchronous()
if self.index_plugin.isFailure():
self.ERROR('indexamajig: Failed')
self.setFailure()
return
else:
self.screen('indexamajig: Finished')
self.process_hkl_plugin.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin_odd.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin_even.dataInput = xsDataInputCrystFEL
self.partialator_plugin.dataInput = xsDataInputCrystFEL
self.post_process_plugin.dataInput = xsDataInputCrystFEL
self.process_hkl_plugin_odd.process_hkl_options += " --odd-only"
self.process_hkl_plugin_even.process_hkl_options += " --even-only"
self.process_hkl_plugin.executeSynchronous()
if self.process_hkl_plugin.isFailure():
self.ERROR('process_hkl: Failed')
self.setFailure()
return
else:
self.screen('process_hkl: Finished')
self.process_hkl_plugin_odd.dataInput.hklFile = XSDataString(self.hklFilename + "_o")
self.process_hkl_plugin_odd.executeSynchronous()
if self.process_hkl_plugin_odd.isFailure():
self.ERROR('process_hkl_odd: Failed')
self.setFailure()
return
else:
self.screen('process_hkl_odd: Finished')
self.process_hkl_plugin_even.dataInput.hklFile = XSDataString(self.hklFilename + "_e")
self.process_hkl_plugin_even.executeSynchronous()
if self.process_hkl_plugin_even.isFailure():
self.ERROR('process_hkl_even: Failed')
self.setFailure()
return
else:
self.screen('process_hkl_even: Finished')
self.partialator_plugin.executeSynchronous()
if self.partialator_plugin.isFailure():
self.ERROR('partialator: Failed')
self.setFailure()
return
else:
self.screen('partialator: Finished')
self.post_process_plugin.executeSynchronous()
if self.post_process_plugin.isFailure():
self.ERROR('post_process: Failed')
self.setFailure()
return
else:
self.screen('post_process: Finished')
"""
self.edPluginExecCrystFELScale.dataInput = xsDataInputCrystFEL
self.edPluginExecCrystFELScale.executeSynchronous()
if self.edPluginExecCrystFELScale.isFailure():
self.ERROR('CrystFELScalev1_0: Failed')
self.setFailure()
return
else:
self.screen('CrystFELScalev1_0: Finished')
self.timeEnd = time.localtime()
"""
# Upload to ISPyB
"""
