def preProcess(self):
EDPluginExecProcessScript.preProcess(self)
self.DEBUG('Pointless: preprocess')
if self.output_file is not None and self.input_file is not None:
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
options = '''-c xdsin {0} hklout {1}'''.format(
self.input_file, self.output_file)
else:
options = '''xdsin {0} hklout {1}'''.format(
self.input_file, self.output_file)
self.setScriptCommandline(options)
self.DEBUG('command line options set to {0}'.format(options))
self.addListCommandExecution('setting symmetry-based')
if self.dataInput.choose_spacegroup is not None:
self.addListCommandExecution('choose spacegroup {0}'.format(
self.dataInput.choose_spacegroup.value))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlRunXdsFastProcv1_0.preProcess")
# Load the execution plugin
self.first_run = self.loadPlugin(self.controlled_plugin_name)
cfg = parse_xds_file(self.dataInput.input_file.value)
spot_range = cfg.get('SPOT_RANGE=')
if spot_range is None:
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
# GB: add a default here - it is nothing worthe then the
# one in autogenerated XDS.INP
pass
else:
strErrorMessage = "No SPOT_RANGE parameter"
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
self.spot_range = spot_range
# we will use this value to constrain the upper bound of
# spot_range so it does not get past the last image number, so
# we use a default value that cannot be a constraint in case
# we cannot find it in the xds input file
self.end_image_no = sys.maxsize
data_range = cfg.get('DATA_RANGE=')
if data_range is not None:
self.start_image_no = data_range[0]
self.end_image_no = data_range[1]
# GB: repair the above.... but why spot_range should be a list of lists?
if spot_range is None:
self.spot_range = [[max(1, data_range[0]),
min(data_range[0] + 99, data_range[1])]]
else:
# Check that spot ranges is within data range
new_spot_range = []
for spot_range in self.spot_range:
if spot_range[0] >= self.start_image_no and spot_range[1] <= self.end_image_no:
new_spot_range.append(spot_range)
self.spot_range = new_spot_range
def __init__(self):
EDLogging.__init__(self)
Thread.__init__(self)
self.__edSlotPreProcess = EDSlot()
self.__edSlotProcess = EDSlot()
self.__edSlotPostProcess = EDSlot()
self.__edSlotSUCCESS = EDSlot()
self.__edSlotFAILURE = EDSlot()
self.__edSlotFinallyProcess = EDSlot()
self.__bIsFailure = False
self.__bIsTimeOut = False
self.__fTimeOutInSeconds = None
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
self.__fDefaultTimeOutInSeconds = 3600.0
else:
self.__fDefaultTimeOutInSeconds = 600.0
self.__bIsAbort = False
# Reference to the object which calls execute or executeSynchronous
self.__edObject = None
self.__lExtraTime = [
] # list of extra allowed time for execution (in second)
self.__bLogTiming = False
def finallyProcess(self, _edPlugin=None):
EDPluginExec.finallyProcess(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev2_1.finallyProcess...")
xsDataResultSimpleHTMLPage = XSDataResultSimpleHTMLPage()
xsDataResultSimpleHTMLPage.setPathToHTMLFile(
XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.strHtmlFileName))))
xsDataResultSimpleHTMLPage.setPathToHTMLDirectory(
XSDataFile(XSDataString(self.getWorkingDirectory())))
# Write workflowStepReport HTML page
pathToIndexFile = self.workflowStepReport.renderHtml(
self.getWorkingDirectory(), nameOfIndexFile=self.strHtmlFileName)
pathToJsonFile = self.workflowStepReport.renderJson(
self.getWorkingDirectory())
# Store in Pyarch
if EDUtilsPath.isESRF() or EDUtilsPath.isEMBL() or EDUtilsPath.isALBA(
) or EDUtilsPath.isMAXIV():
strPyarchPath = None
if self.xsDataResultCharacterisation is not None:
strPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchHtmlDirectoryPath(
self.xsDataResultCharacterisation.getDataCollection())
if strPyarchPath is None:
# For debugging purposes
strPyarchPath = EDUtilsPath.getEdnaUserTempFolder()
EDHandlerESRFPyarchv1_0.copyHTMLDir(
_strPathToHTMLDir=os.path.dirname(self.strPath),
_strPathToPyarchDirectory=strPyarchPath)
xsDataResultSimpleHTMLPage.setPathToHTMLDirectory(
XSDataFile(XSDataString(strPyarchPath)))
shutil.copy(pathToJsonFile, strPyarchPath)
pathToJsonFile = os.path.join(strPyarchPath,
os.path.basename(pathToJsonFile))
# Write json file
xsDataResultSimpleHTMLPage.pathToJsonFile = XSDataFile(
XSDataString(pathToJsonFile))
self.setDataOutput(xsDataResultSimpleHTMLPage)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlPyarchThumbnailGeneratorv1_0.preProcess")
# Check that the input image exists and is of the expected type
strPathToDiffractionImage = self.dataInput.diffractionImage.path.value
strImageFileNameExtension = os.path.splitext(
strPathToDiffractionImage)[1]
if not strImageFileNameExtension in [
".img", ".marccd", ".mccd", ".cbf", ".h5"
]:
self.error(
"Unknown image file name extension for pyarch thumbnail generator: %s"
% strPathToDiffractionImage)
self.setFailure()
else:
# Load the MXWaitFile plugin
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
pathToImageFile = strPathToDiffractionImage
# Quite ugly hack to avoid lag problems at the ESRF:
if EDUtilsPath.isESRF() or EDUtilsPath.isALBA():
if any(beamline in strPathToDiffractionImage
for beamline in ["id23eh1", "id29", "id30b"]):
# Pilatus 6M
self.minImageSize = 6000000
elif any(beamline in strPathToDiffractionImage
for beamline in ["id23eh2", "id30a1"]):
# Pilatus3 2M
self.minImageSize = 2000000
elif strImageFileNameExtension == ".h5":
self.h5MasterFilePath, self.h5DataFilePath, self.h5FileNumber = self.getH5FilePath(
pathToImageFile)
pathToImageFile = self.h5DataFilePath
self.isH5 = True
elif EDUtilsPath.isEMBL():
self.minImageSize = 10000
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setFile(
XSDataFile(XSDataString(pathToImageFile)))
if self.getDataInput().getWaitForFileTimeOut():
xsDataInputMXWaitFile.setTimeOut(
self.getDataInput().getWaitForFileTimeOut())
self.edPluginMXWaitFile = self.loadPlugin(
self.strMXWaitFilePluginName)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
# Load the execution plugin
self.edPluginExecThumbnail = self.loadPlugin(
self.strExecThumbnailPluginName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = self.getDataInput(
).getDiffractionImage()
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
xsDataInputMXThumbnail.format = self.dataInput.format
# Output path
strImageNameWithoutExt = os.path.basename(
os.path.splitext(strPathToDiffractionImage)[0])
strImageDirname = os.path.dirname(strPathToDiffractionImage)
if self.getDataInput().getForcedOutputDirectory():
strForcedOutputDirectory = self.getDataInput(
).getForcedOutputDirectory().getPath().getValue()
if not os.access(strForcedOutputDirectory, os.W_OK):
self.error("Cannot write to forced output directory : %s" %
strForcedOutputDirectory)
self.setFailure()
else:
self.strOutputPathWithoutExtension = os.path.join(
strForcedOutputDirectory, strImageNameWithoutExt)
else:
# Try to store in the ESRF pyarch directory
strOutputDirname = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
strImageDirname)
# Check that output pyarch path exists and is writeable:
bIsOk = False
if strOutputDirname:
if not os.path.exists(strOutputDirname):
# Try to create the directory
try:
os.makedirs(strOutputDirname)
bIsOk = True
except Exception as e:
self.WARNING("Couldn't create the directory %s" %
strOutputDirname)
elif os.access(strOutputDirname, os.W_OK):
bIsOk = True
if not bIsOk:
self.warning("Cannot write to pyarch directory: %s" %
strOutputDirname)
strTmpUser = os.path.join("/tmp", os.environ["USER"])
if not os.path.exists(strTmpUser):
os.mkdir(strTmpUser, 0o755)
strOutputDirname = tempfile.mkdtemp(
prefix="EDPluginPyarchThumbnailv10_", dir=strTmpUser)
os.chmod(strOutputDirname, 0o755)
self.warning("Writing thumbnail images to: %s" %
strOutputDirname)
self.strOutputPathWithoutExtension = os.path.join(
strOutputDirname, strImageNameWithoutExt)
if self.dataInput.format is not None:
self.strSuffix = self.dataInput.format.value.lower()
self.strImageFormat = self.dataInput.format.value.upper()
self.strOutputPath = os.path.join(
self.strOutputPathWithoutExtension + "." + self.strSuffix)
xsDataInputMXThumbnail.setOutputPath(
XSDataFile(XSDataString(self.strOutputPath)))
self.edPluginExecThumbnail.setDataInput(xsDataInputMXThumbnail)
def process(self):
self.DEBUG('FileConversion: process')
EDPluginControl.process(self)
# first we generate the intermediary file name
pointless_in = XSDataPointless()
pointless_in.input_file = self.dataInput.input_file
pointless_out = os.path.join(os.path.dirname(self.dataInput.output_file.value),
self.pointless_out)
pointless_in.output_file = XSDataString(pointless_out)
if self.dataInput.choose_spacegroup is not None:
pointless_in.choose_spacegroup = self.dataInput.choose_spacegroup
self.pointless.dataInput = pointless_in
self.screen("Pointless run " + self.strAnomSuffix)
self.pointless.executeSynchronous()
if self.pointless.isFailure():
strErrorMessage = "Pointless {0} failed".format(self.strAnomSuffix)
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
aimless_in = XSDataAimless()
aimless_in.input_file = pointless_in.output_file
aimless_in.output_file = XSDataString(os.path.join(self.results_dir,
self.aimless_out))
aimless_in.command_file = XSDataString(os.path.join(self.results_dir,
self.aimless_commands_out))
aimless_in.dataCollectionID = self.dataInput.dataCollectionID
aimless_in.start_image = self.dataInput.start_image
aimless_in.end_image = self.dataInput.end_image
aimless_in.res = self.dataInput.res
aimless_in.anom = self.dataInput.anom
self.aimless.dataInput = aimless_in
self.screen("Aimless run " + self.strAnomSuffix)
self.aimless.executeSynchronous()
if self.aimless.isFailure():
strErrorMessage = "Aimless {0} failed".format(self.strAnomSuffix)
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
# copy the aimless log where the results files are
source_log = os.path.join(self.aimless.getWorkingDirectory(),
self.aimless.getScriptLogFileName())
self.aimless_log = source_log
target_log = os.path.join(self.results_dir,
'ep_{0}aimless_{1}.log'.format(self.image_prefix,
"anom" if self.dataInput.anom.value else "noanom"))
try:
shutil.copyfile(source_log, target_log)
except IOError:
self.ERROR('Could not copy aimless log file from {0} to {1}'.format(source_log,
target_log))
# now truncate
truncate_in = XSDataTruncate()
truncate_in.input_file = self.aimless.dataInput.output_file
temp_file = tempfile.NamedTemporaryFile(suffix='.mtz',
prefix='tmp2-',
dir=self.aimless.getWorkingDirectory(),
delete=False)
truncate_out = temp_file.name
temp_file.close()
os.chmod(truncate_out, S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH)
truncate_in.output_file = XSDataString(truncate_out)
truncate_in.nres = self.dataInput.nres
truncate_in.anom = self.dataInput.anom
truncate_in.res = self.dataInput.res
self.truncate.dataInput = truncate_in
self.screen("Truncate run " + self.strAnomSuffix)
self.truncate.executeSynchronous()
if self.truncate.isFailure():
strErrorMessage = "Truncate {0} failed".format(self.strAnomSuffix)
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
# copy the truncate log where the results files are
source_log = os.path.join(self.truncate.getWorkingDirectory(),
self.truncate.getScriptLogFileName())
target_log = os.path.join(self.results_dir,
'ep_{0}truncate_{1}.log'.format(self.image_prefix,
"anom" if self.dataInput.anom.value else "noanom"))
try:
shutil.copyfile(source_log,
target_log)
except IOError:
self.ERROR('Could not copy truncate log file from {0} to {1}'.format(source_log,
target_log))
# and finally uniqueify
uniqueify_in = XSDataUniqueify()
uniqueify_in.input_file = truncate_in.output_file
uniqueify_out = os.path.join(self.results_dir,
self.truncate_out)
uniqueify_in.output_file = XSDataString(uniqueify_out)
self.uniqueify.dataInput = uniqueify_in
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
# GB: skipping misteriously failing uniqueify run -
# which is useless anyway.
# copying temp truncate output to results directly
shutil.copyfile(uniqueify_in.input_file.value, uniqueify_out)
return
self.screen("Uniqueify run " + self.strAnomSuffix)
self.uniqueify.executeSynchronous()
if self.uniqueify.isFailure():
strErrorMessage = "Uniqueify {0} failed".format(self.strAnomSuffix)
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
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 generateCommandLine(self, _xsDataInputAutoPROC):
"""
This method creates the input command line for autoPROC
"""
self.DEBUG("EDPluginExecAutoPROCv1_0.generateCommands")
strCommandText = "-B -xml -nthreads {0} -M ReportingInlined autoPROC_HIGHLIGHT=\"no\"".format(self.maxNoProcessors)
if self.doScaleWithXscale:
strCommandText += " autoPROC_ScaleWithXscale='yes'"
if self.rotationAxis is not None:
strCommandText += " autoPROC_XdsKeyword_ROTATION_AXIS=\"{0}\"".format(self.rotationAxis)
# Master H5 file
masterH5 = _xsDataInputAutoPROC.masterH5
if masterH5 is None:
# Identifier(s)
for identifier in _xsDataInputAutoPROC.identifier:
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
identifier.templateN.value = identifier.templateN.value.replace(\
'%' + '05' + 'd', 5 * '#')
strCommandText += " -Id {idN},{dirN},{templateN},{fromN},{toN}".format(
idN=identifier.idN.value,
dirN=identifier.dirN.path.value,
templateN=identifier.templateN.value,
fromN=identifier.fromN.value,
toN=identifier.toN.value)
else:
strCommandText += " -h5 {0}".format(masterH5.path.value)
if self.pathToNeggiaPlugin is not None:
strCommandText += " autoPROC_XdsKeyword_LIB={0}".format(self.pathToNeggiaPlugin)
# Resolution
lowResolutionLimit = _xsDataInputAutoPROC.lowResolutionLimit
highResolutionLimit = _xsDataInputAutoPROC.highResolutionLimit
if lowResolutionLimit is not None or highResolutionLimit is not None:
# See https://www.globalphasing.com/autoproc/manual/autoPROC4.html#processcli
if lowResolutionLimit is None:
low = 1000.0 # autoPROC default value
else:
low = lowResolutionLimit.value
if highResolutionLimit is None:
high = 0.1 # autoPROC default value
else:
high = highResolutionLimit.value
strCommandText += " -R {0} {1}".format(low, high)
# Anomalous
anomalous = _xsDataInputAutoPROC.anomalous
if anomalous is not None:
if anomalous.value:
strCommandText += " -ANO"
# Reference MTZ file
refMTZ = _xsDataInputAutoPROC.refMTZ
if refMTZ is not None:
strCommandText += " -ref {0}".format(refMTZ.path.value)
# Forced space group
if _xsDataInputAutoPROC.symm is not None:
strCommandText += " symm=\"{0}\"".format(_xsDataInputAutoPROC.symm.value)
# Forced cell
if _xsDataInputAutoPROC.cell is not None:
strCommandText += " cell=\"{0}\"".format(_xsDataInputAutoPROC.cell.value)
return strCommandText
def generateCommands(self, _xsDataInputH5ToCBF):
"""
This method creates a list of commands for the converter
"""
self.DEBUG("EDPluginH5ToCBFv1_1.generateCommands")
hdf5File = _xsDataInputH5ToCBF.hdf5File.path.value
directory = os.path.dirname(hdf5File)
prefix = EDUtilsImage.getPrefix(hdf5File)
if _xsDataInputH5ToCBF.imageNumber is not None:
imageNumber = _xsDataInputH5ToCBF.imageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA():
masterFile = os.path.join(
directory,
prefix + "_master.h5".format(hdf5ImageNumber))
else:
masterFile = os.path.join(
directory,
prefix + "_{0}_master.h5".format(hdf5ImageNumber))
if _xsDataInputH5ToCBF.forcedOutputImageNumber is not None:
CBFFileName = prefix + "_%04d" % _xsDataInputH5ToCBF.forcedOutputImageNumber.value + ".cbf"
imageNumberInHdf5File = imageNumber
else:
CBFFileName = prefix + "_%04d" % imageNumber + ".cbf"
imageNumberInHdf5File = imageNumber - hdf5ImageNumber + 1
tmpCBFFileName = "tmp_" + CBFFileName
if _xsDataInputH5ToCBF.forcedOutputDirectory is None:
self.CBFFile = os.path.join(directory, CBFFileName)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0o755)
self.CBFFile = os.path.join(forcedOutputDirectory, CBFFileName)
scriptCommandLine = "{0} {1} {2}".format(masterFile,
imageNumberInHdf5File,
self.CBFFile)
elif _xsDataInputH5ToCBF.startImageNumber is not None and _xsDataInputH5ToCBF.endImageNumber is not None:
startImageNumber = _xsDataInputH5ToCBF.startImageNumber.value
endImageNumber = _xsDataInputH5ToCBF.endImageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = startImageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
masterFile = os.path.join(
directory,
prefix + "_{0}_master.h5".format(hdf5ImageNumber))
CBFFileNamePrefix = prefix + "_"
if _xsDataInputH5ToCBF.forcedOutputDirectory is None:
CBFFilePath = os.path.join(directory, CBFFileNamePrefix)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0o755)
CBFFilePath = os.path.join(forcedOutputDirectory,
CBFFileNamePrefix)
scriptCommandLine = "{0} {1}:{2} {3}".format(
masterFile, startImageNumber, endImageNumber, CBFFilePath)
self.CBFFileTemplate = CBFFilePath + "######.cbf"
return scriptCommandLine
def createPyarchFilePath(_strESRFPath):
"""
This method translates from an ESRF "visitor" path to a "pyarch" path:
/data/visitor/mx415/id14eh1/20100209 -> /data/pyarch/2010/id14eh1/mx415/20100209
"""
strPyarchDNAFilePath = None
listOfDirectories = _strESRFPath.split(os.sep)
if EDUtilsPath.isALBA():
return EDHandlerESRFPyarchv1_0.translateToIspybALBAPath(
_strESRFPath)
if EDUtilsPath.isEMBL():
if 'p13' in listOfDirectories[0:3] or 'P13' in listOfDirectories[
0:3]:
strPyarchDNAFilePath = os.path.join('/data/ispyb/p13',
*listOfDirectories[4:])
else:
strPyarchDNAFilePath = os.path.join('/data/ispyb/p14',
*listOfDirectories[4:])
return strPyarchDNAFilePath
if EDUtilsPath.isMAXIV():
strPyarchDNAFilePath = _strESRFPath.replace(
"/data", "/mxn/groups/ispybstorage", 1)
return strPyarchDNAFilePath
listBeamlines = [
"bm07", "id14eh1", "id14eh2", "id14eh3", "id14eh4", "id23eh1",
"id23eh2", "id29", "id30a1", "id30a2", "id30a3", "id30b",
"simulator_mxcube"
]
# Check that we have at least four levels of directories:
if (len(listOfDirectories) > 5):
strDataDirectory = listOfDirectories[1]
strSecondDirectory = listOfDirectories[2]
strThirdDirectory = listOfDirectories[3]
strFourthDirectory = listOfDirectories[4]
strFifthDirectory = listOfDirectories[5]
year = strFifthDirectory[0:4]
strProposal = None
strBeamline = None
if (strDataDirectory == "data") and (strSecondDirectory == "gz"):
if strThirdDirectory == "visitor":
strProposal = strFourthDirectory
strBeamline = strFifthDirectory
elif strFourthDirectory == "inhouse":
strProposal = strFifthDirectory
strBeamline = strThirdDirectory
else:
raise RuntimeError(
"Illegal path for EDHandlerESRFPyarchv1_0.createPyarchFilePath: {0}"
.format(_strESRFPath))
listOfRemainingDirectories = listOfDirectories[6:]
elif (strDataDirectory == "data") and (strSecondDirectory
== "visitor"):
strProposal = listOfDirectories[3]
strBeamline = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
elif ((strDataDirectory == "data")
and (strSecondDirectory in listBeamlines)):
strBeamline = strSecondDirectory
strProposal = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
if (strProposal != None) and (strBeamline != None):
strPyarchDNAFilePath = os.path.join(os.sep, "data")
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
"pyarch")
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath, year)
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
strBeamline)
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
strProposal)
for strDirectory in listOfRemainingDirectories:
strPyarchDNAFilePath = os.path.join(
strPyarchDNAFilePath, strDirectory)
if (strPyarchDNAFilePath is None):
EDVerbose.WARNING(
"EDHandlerESRFPyarchv1_0.createPyArchFilePath: path not converted for pyarch: %s "
% _strESRFPath)
return strPyarchDNAFilePath
