def doSuccessMXWaitFile(self, _edPlugin=None): self.DEBUG("EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile") self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile") # Check that the image is really there if not self.edPluginMXWaitFile.dataOutput.timedOut.value: # Workaround for ESRF lag problem if EDUtilsPath.isESRF(): time.sleep(2) if self.isH5: diffractionImagePath = self.dataInput.diffractionImage.path.value imageNumber = EDUtilsImage.getImageNumber(diffractionImagePath) xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF() xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(diffractionImagePath)) xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber) xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(self.h5FileNumber) xsDataInputControlH5ToCBF.ispybDataCollection = None xsDataInputControlH5ToCBF.forcedOutputDirectory = XSDataFile(XSDataString(self.getWorkingDirectory())) edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_{0:04d}".format(imageNumber)) edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF edPluginControlH5ToCBF.executeSynchronous() cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile self.edPluginExecThumbnail.dataInput.image = cbfFile # The image is here - make the first thumbnail self.edPluginExecThumbnail.connectSUCCESS(self.doSuccessExecThumbnail) self.edPluginExecThumbnail.connectFAILURE(self.doFailureExecThumbnail) self.edPluginExecThumbnail.executeSynchronous() else: self.error("Time-out while waiting for image!") self.setFailure()
def finallyProcess(self, _edPlugin=None): EDPluginExec.finallyProcess(self, _edPlugin) self.DEBUG("EDPluginExecSimpleHTMLPagev1_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(): 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))) if not os.path.exists(strPyarchPath): os.makedirs(strPyarchPath, 0o755) 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 createApplicationWorkingDirectory(self): """ Created the working directory of the application (<date>-<application name>) First tries to retrieve the base dir from --basedir option or related parameter from constructor Otherwise tries to retrieve it from EDNA_BASE_DIRECTORY environment variable Otherwise put the base dir as the current directory """ EDVerbose.DEBUG("EDApplication.createApplicationWorkingDirectory") strBaseDirectory = self.getBaseDir() strDateTime = time.strftime("%Y%m%d-%H%M%S", time.localtime(time.time())) self._strFullApplicationWorkingDirectory = os.path.join(strBaseDirectory, self._strWorkingDir) # Check that a folder / file with the same name already exists if(os.path.exists(self._strFullApplicationWorkingDirectory) or \ os.path.exists(self._strFullApplicationWorkingDirectory)): # It does exist so we have to modify the name of the working directory iIndex = 1 bContinueFlag = True while (bContinueFlag): self._strFullApplicationWorkingDirectory = os.path.join(strBaseDirectory, "%s_%d" % \ (strDateTime, \ iIndex)) if(os.path.isdir(self._strFullApplicationWorkingDirectory) or \ os.path.exists(self._strFullApplicationWorkingDirectory)): iIndex += 1 else: bContinueFlag = False # Add _nobackup suffix if run at the ESRF strEdnSite = EDUtilsPath.getEdnaSite() if EDUtilsPath.isESRF(): self._strFullApplicationWorkingDirectory += "_nobackup" # Make the directory os.mkdir(self._strFullApplicationWorkingDirectory) # Change it to be the current working directory os.chdir(self._strFullApplicationWorkingDirectory)
def process(self, _edObject=None): EDPluginExec.process(self) self.DEBUG("EDPluginExecPlotGlev1_1.process") for dictPlot in self.listPlot: if os.path.dirname(dictPlot["script"]) != self.getWorkingDirectory(): shutil.copy(dictPlot["script"], self.getWorkingDirectory()) listDataFiles = dictPlot["data"] for strDataFileFullPath in listDataFiles: strDataFile = os.path.basename(strDataFileFullPath) if not os.path.exists(os.path.join(self.getWorkingDirectory(), strDataFile)): shutil.copy(strDataFileFullPath, self.getWorkingDirectory()) if EDUtilsPath.isESRF(): # Force PXSOFT version of gle strCommand = "/opt/pxsoft/bin/gle -verbosity 0 -r 150 -d jpg %s" % os.path.basename(dictPlot["script"]) else: strCommand = "gle -verbosity 0 -r 150 -d jpg %s" % os.path.basename(dictPlot["script"]) # Copied from EDPluginExecProcess self.DEBUG(self.getBaseName() + ": Processing") timer = threading.Timer(float(self.getTimeOut()), self.kill) timer.start() try: self.__subprocess = EDUtilsPlatform.Popen(shlex.split(str(EDUtilsPlatform.escape(strCommand))), cwd=self.getWorkingDirectory()) self.__iPID = self.__subprocess.pid self.__strExecutionStatus = str(self.__subprocess.wait()) except OSError as e: strErrorMessage = self.getPluginName() + " : required program gle not installed" self.error(strErrorMessage) self.setFailure() finally: timer.cancel()
def finallyProcess(self, _edPlugin=None): EDPluginExec.finallyProcess(self, _edPlugin) self.DEBUG("EDPluginExecSimpleHTMLPagev1_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.isMAXIV() or EDUtilsPath.isALBA: 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))) if not os.path.exists(strPyarchPath): os.makedirs(strPyarchPath, 0o755) 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 sendEmail(self, _strSubject, _strMessage): """Sends an email to the EDNA contact person (if configured).""" strTime = "%.1f s" % (self.tStop - self.tStart) if EDUtilsPath.isESRF(): strPathImage = None for dataSet in self.dataInput.dataSet: for imageFile in dataSet.imageFile: strPathImage = imageFile.path.value break if strPathImage is not None: (strBeamline, strProposal, strPrefix) = self.getBeamlineProposalFromPath(strPathImage) else: strBeamline = "Unknown" strProposal = "Unknown" strPrefix = "Unknown" strHost = socket.gethostname() strSubject = "EDNA ch %s %s %s %s %s (%s)" % (_strSubject, strBeamline, strProposal, strPrefix, strHost, strTime) else: strSubject = "EDNA %s : %s (%s)" % (_strSubject, EDUtilsPath.getEdnaSite(), strTime) self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.sendEmail: Subject = %s" % strSubject) self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.sendEmail: Message:") self.DEBUG(_strMessage) if self.strEDNAContactEmail == None: self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.sendEmail: No email address configured!") elif not EDUtilsPath.getEdnaSite().startswith("ESRF"): self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.sendEmail: Not executed at the ESRF! EDNA_SITE=%s" % EDUtilsPath.getEdnaSite()) else: try: self.DEBUG("Sending message to %s." % self.strEDNAContactEmail) self.DEBUG("Message: %s" % _strMessage) strMessage = "EDNA_HOME = %s\n" % EDUtilsPath.getEdnaHome() strMessage += "EDNA_SITE = %s\n" % EDUtilsPath.getEdnaSite() strMessage += "PLUGIN_NAME = %s\n" % self.getPluginName() strMessage += "working_dir = %s\n\n" % self.getWorkingDirectory() strMessage += "Reference images:\n" xsDataInputMXCuBE = self.getDataInput() for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet(): for xsDataFile in xsDataSetMXCuBE.getImageFile(): strMessage += "%s\n" % xsDataFile.getPath().getValue() strMessage += "\n" strMessage += _strMessage strEmailMsg = ("From: %s\r\nTo: %s\r\nSubject: %s\r\n\r\n%s" % (self.strEDNAEmailSender, \ self.strEDNAContactEmail, \ strSubject, strMessage)) server = smtplib.SMTP("localhost") server.sendmail(self.strEDNAEmailSender, self.strEDNAContactEmail, strEmailMsg) server.quit() except: self.ERROR("Error when sending email message!") self.writeErrorTrace()
def sendEmail(self, _strSubject, _strMessage): """Sends an email to the EDNA contact person (if configured).""" strTime = "%.1f s" % (self.tStop - self.tStart) if EDUtilsPath.isESRF(): strPathImage = None for dataSet in self.dataInput.dataSet: for imageFile in dataSet.imageFile: strPathImage = imageFile.path.value break if strPathImage is not None: (strBeamline, strProposal, strPrefix) = self.getBeamlineProposalFromPath(strPathImage) else: strBeamline = "Unknown" strProposal = "Unknown" strPrefix = "Unknown" strHost = socket.gethostname() strSubject = "EDNA ch %s %s %s %s %s (%s)" % (_strSubject, strBeamline, strProposal, strPrefix, strHost, strTime) else: strSubject = "EDNA %s : %s (%s)" % (_strSubject, EDUtilsPath.getEdnaSite(), strTime) self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.sendEmail: Subject = %s" % strSubject) self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.sendEmail: Message:") self.DEBUG(_strMessage) if self.strEDNAContactEmail == None: self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.sendEmail: No email address configured!") elif not EDUtilsPath.getEdnaSite().startswith("ESRF"): self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_3.sendEmail: Not executed at the ESRF! EDNA_SITE=%s" % EDUtilsPath.getEdnaSite()) else: try: self.DEBUG("Sending message to %s." % self.strEDNAContactEmail) self.DEBUG("Message: %s" % _strMessage) strMessage = "EDNA_HOME = %s\n" % EDUtilsPath.getEdnaHome() strMessage += "EDNA_SITE = %s\n" % EDUtilsPath.getEdnaSite() strMessage += "PLUGIN_NAME = %s\n" % self.getPluginName() strMessage += "working_dir = %s\n\n" % self.getWorkingDirectory() strMessage += "Reference images:\n" xsDataInputMXCuBE = self.getDataInput() for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet(): for xsDataFile in xsDataSetMXCuBE.getImageFile(): strMessage += "%s\n" % xsDataFile.getPath().getValue() strMessage += "\n" strMessage += _strMessage strEmailMsg = ("From: %s\r\nTo: %s\r\nSubject: %s\r\n\r\n%s" % (self.strEDNAEmailSender, \ self.strEDNAContactEmail, \ strSubject, strMessage)) server = smtplib.SMTP("localhost") server.sendmail(self.strEDNAEmailSender, self.strEDNAContactEmail, strEmailMsg) server.quit() except: self.ERROR("Error when sending email message!") self.writeErrorTrace()
def parse_xds_file(path): parsed = dict() loaded = _load_xds_file(path) # Workaround for problem in ESRF XDS.INP generation during burn strategy workflow execution if EDUtilsPath.isESRF(): has_added_spot_range = False tmp_loaded = [] for kw, args in loaded: if kw == "DATA_RANGE=": data_range = args tmp_loaded.append((kw, args)) elif kw == "SPOT_RANGE=": if len(args) == 2: tmp_loaded.append((kw, args)) has_added_spot_range = True else: tmp_loaded.append((kw, args)) if not has_added_spot_range: tmp_loaded.insert(2, ("SPOT_RANGE=", data_range)) loaded = tmp_loaded # pythonize the arguments for kw, args in loaded: if kw not in CONFIGURATION_PARSERS: # XXX maybe log it continue parser = CONFIGURATION_PARSERS[kw] # print 'parsing', args, 'with', parser, 'for kw', kw # XXX maybe catch exc and log them parsedargs = parser(args) # special case, for repeatable params, we add them as a list # or append them if they already exist if kw in REPEATABLE_PARAMS: # print 'keyword', kw, 'is repeatable' if kw in parsed: parsed[kw].append(parsedargs) else: parsed[kw] = [parsedargs] else: # regular case just assign the thing parsed[kw] = parsedargs return parsed
def parse_xds_file(path): parsed = dict() loaded = _load_xds_file(path) # Workaround for problem in ESRF XDS.INP generation during burn strategy workflow execution if EDUtilsPath.isESRF(): has_added_spot_range = False tmp_loaded = [] for kw, args in loaded: if kw == "DATA_RANGE=": data_range = args tmp_loaded.append((kw, args)) elif kw == "SPOT_RANGE=": if len(args) == 2: tmp_loaded.append((kw, args)) has_added_spot_range = True else: tmp_loaded.append((kw, args)) if not has_added_spot_range: tmp_loaded.insert(2, ("SPOT_RANGE=", data_range)) loaded = tmp_loaded # pythonize the arguments for kw, args in loaded: if kw not in CONFIGURATION_PARSERS: # XXX maybe log it continue parser = CONFIGURATION_PARSERS[kw] #print 'parsing', args, 'with', parser, 'for kw', kw # XXX maybe catch exc and log them parsedargs = parser(args) # special case, for repeatable params, we add them as a list # or append them if they already exist if kw in REPEATABLE_PARAMS: #print 'keyword', kw, 'is repeatable' if kw in parsed: parsed[kw].append(parsedargs) else: parsed[kw] = [parsedargs] else: # regular case just assign the thing parsed[kw] = parsedargs return parsed
def doSuccessMXWaitFile(self, _edPlugin=None): self.DEBUG( "EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile") self.retrieveSuccessMessages( _edPlugin, "EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile") # Check that the image is really there if not self.edPluginMXWaitFile.dataOutput.timedOut.value: # Workaround for ESRF lag problem if EDUtilsPath.isESRF(): time.sleep(2) if self.isH5: diffractionImagePath = self.dataInput.diffractionImage.path.value imageNumber = EDUtilsImage.getImageNumber( diffractionImagePath) xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF() xsDataInputControlH5ToCBF.hdf5File = XSDataFile( XSDataString(diffractionImagePath)) xsDataInputControlH5ToCBF.imageNumber = XSDataInteger( imageNumber) xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger( self.h5FileNumber) xsDataInputControlH5ToCBF.ispybDataCollection = None xsDataInputControlH5ToCBF.forcedOutputDirectory = XSDataFile( XSDataString(self.getWorkingDirectory())) edPluginControlH5ToCBF = self.loadPlugin( self.strPluginControlH5ToCBF, "ControlH5ToCBF_{0:04d}".format(imageNumber)) edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF edPluginControlH5ToCBF.executeSynchronous() cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile self.edPluginExecThumbnail.dataInput.image = cbfFile # The image is here - make the first thumbnail self.edPluginExecThumbnail.connectSUCCESS( self.doSuccessExecThumbnail) self.edPluginExecThumbnail.connectFAILURE( self.doFailureExecThumbnail) self.edPluginExecThumbnail.executeSynchronous() else: self.error("Time-out while waiting for image!") self.setFailure()
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 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, _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 postProcess(self, _edObject=None): EDPluginControl.postProcess(self) self.DEBUG("EDPluginControlDozorv1_0.postProcess") # Write a file to be used with ISPyB or GNUPLOT only if data collection id in input dataCollectionId = None if self.dataInput.dataCollectionId is None and len(self.dataInput.image) > 0: # Only try to obtain data collection id if at the ESRF and path starts with "/data" if EDUtilsPath.isESRF() and self.dataInput.image[0].path.value.startswith("/data"): xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection() xsDataInputRetrieveDataCollection.image = XSDataImage(self.dataInput.image[0].path) 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: dataCollectionId = dataCollection.dataCollectionId elif self.dataInput.dataCollectionId is not None: dataCollectionId = self.dataInput.dataCollectionId.value if dataCollectionId is not None: minImageNumber = None maxImageNumber = None minAngle = None maxAngle = None minDozorValue = None maxDozorValue = None minResolution = None maxResolution = None dozorPlotFileName = "dozor_{0}.png".format(dataCollectionId) dozorCsvFileName = "dozor_{0}.csv".format(dataCollectionId) with open(os.path.join(self.getWorkingDirectory(), dozorCsvFileName), "w") as gnuplotFile: gnuplotFile.write("# Data directory: {0}\n".format(self.directory)) gnuplotFile.write("# File template: {0}\n".format(self.template.replace("%04d", "####"))) gnuplotFile.write("# {0:>9s}{1:>16s}{2:>16s}{3:>16s}{4:>16s}{5:>16s}\n".format("'Image no'", "'Angle'", "'No of spots'", "'Main score (*10)'", "'Spot score'", "'Visible res.'", )) for imageDozor in self.dataOutput.imageDozor: gnuplotFile.write("{0:10d},{1:15.3f},{2:15d},{3:15.3f},{4:15.3f},{5:15.3f}\n".format(imageDozor.number.value, imageDozor.angle.value, imageDozor.spotsNumOf.value, 10 * imageDozor.mainScore.value, imageDozor.spotScore.value, imageDozor.visibleResolution.value, )) if minImageNumber is None or minImageNumber > imageDozor.number.value: minImageNumber = imageDozor.number.value minAngle = imageDozor.angle.value if maxImageNumber is None or maxImageNumber < imageDozor.number.value: maxImageNumber = imageDozor.number.value maxAngle = imageDozor.angle.value if minDozorValue is None or minDozorValue > imageDozor.mainScore.value: minDozorValue = imageDozor.spotScore.value if maxDozorValue is None or maxDozorValue < imageDozor.mainScore.value: maxDozorValue = imageDozor.spotScore.value # Min resolution: the higher the value the lower the resolution if minResolution is None or minResolution < imageDozor.visibleResolution.value: # Disregard resolution worse than 10.0 if imageDozor.visibleResolution.value < 10.0: minResolution = imageDozor.visibleResolution.value # Max resolution: the lower the number the better the resolution if maxResolution is None or maxResolution > imageDozor.visibleResolution.value: maxResolution = imageDozor.visibleResolution.value xtics = "" if minImageNumber is not None and minImageNumber == maxImageNumber: minAngle -= 1.0 maxAngle += 1.0 noImages = maxImageNumber - minImageNumber + 1 if noImages <= 4: minImageNumber -= 0.1 maxImageNumber += 0.1 deltaAngle = maxAngle - minAngle minAngle -= deltaAngle * 0.1 / noImages maxAngle += deltaAngle * 0.1 / noImages xtics = "1" if maxResolution is None or maxResolution > 0.8: maxResolution = 0.8 else: maxResolution = int(maxResolution * 10.0) / 10.0 if minResolution is None or minResolution < 4.5: minResolution = 4.5 else: minResolution = int(minResolution * 10.0) / 10.0 + 1 if maxDozorValue < 0.001 and minDozorValue < 0.001: yscale = "set yrange [-0.5:0.5]\n set ytics 1" else: yscale = "set autoscale y" gnuplotFile.close() gnuplotScript = \ """# set terminal png set output '{dozorPlotFileName}' set title '{title}' set grid x2 y2 set xlabel 'Image number' set x2label 'Angle (degrees)' set y2label 'Resolution (A)' set ylabel 'Number of spots / Dozor score (*10)' set xtics {xtics} nomirror set x2tics set ytics nomirror set y2tics set xrange [{minImageNumber}:{maxImageNumber}] set x2range [{minAngle}:{maxAngle}] {yscale} set y2range [{minResolution}:{maxResolution}] set key below plot '{dozorCsvFileName}' using 1:3 title 'Number of spots' axes x1y1 with points linetype rgb 'goldenrod' pointtype 7 pointsize 1.5, \ '{dozorCsvFileName}' using 1:4 title 'Dozor score' axes x1y1 with points linetype 3 pointtype 7 pointsize 1.5, \ '{dozorCsvFileName}' using 1:6 title 'Visible resolution' axes x1y2 with points linetype 1 pointtype 7 pointsize 1.5 """.format(title=self.template.replace("%04d", "####"), dozorPlotFileName=dozorPlotFileName, dozorCsvFileName=dozorCsvFileName, minImageNumber=minImageNumber, maxImageNumber=maxImageNumber, minAngle=minAngle, maxAngle=maxAngle, minResolution=minResolution, maxResolution=maxResolution, xtics=xtics, yscale=yscale, ) pathGnuplotScript = os.path.join(self.getWorkingDirectory(), "gnuplot.sh") data_file = open(pathGnuplotScript, "w") data_file.write(gnuplotScript) data_file.close() oldCwd = os.getcwd() os.chdir(self.getWorkingDirectory()) os.system("{0} {1}".format(self.gnuplot, pathGnuplotScript)) os.chdir(oldCwd) self.dataOutput.dozorPlot = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), dozorPlotFileName))) if self.dataInput.processDirectory is not None: processDirectory = self.dataInput.processDirectory.path.value else: processDirectory = os.path.join(self.directory.replace("RAW_DATA", "PROCESSED_DATA"), "DozorPlot") resultsDirectory = os.path.join(processDirectory, "results") dozorPlotResultPath = os.path.join(resultsDirectory, dozorPlotFileName) dozorCsvResultPath = os.path.join(resultsDirectory, dozorCsvFileName) try: if not os.path.exists(resultsDirectory): os.makedirs(resultsDirectory, 0o755) shutil.copy(os.path.join(self.getWorkingDirectory(), dozorPlotFileName), dozorPlotResultPath) shutil.copy(os.path.join(self.getWorkingDirectory(), dozorCsvFileName), dozorCsvResultPath) except: self.warning("Couldn't copy files to results directory: {0}".format(resultsDirectory)) try: # Create paths on pyarch dozorPlotPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(dozorPlotResultPath) dozorCsvPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(dozorCsvResultPath) if not os.path.exists(os.path.dirname(dozorPlotPyarchPath)): os.makedirs(os.path.dirname(dozorPlotPyarchPath), 0o755) shutil.copy(dozorPlotResultPath, dozorPlotPyarchPath) shutil.copy(dozorCsvResultPath, dozorCsvPyarchPath) # Upload to data collection xsDataInputISPyBSetImageQualityIndicatorsPlot = XSDataInputISPyBSetImageQualityIndicatorsPlot() xsDataInputISPyBSetImageQualityIndicatorsPlot.dataCollectionId = XSDataInteger(dataCollectionId) xsDataInputISPyBSetImageQualityIndicatorsPlot.imageQualityIndicatorsPlotPath = XSDataString(dozorPlotPyarchPath) xsDataInputISPyBSetImageQualityIndicatorsPlot.imageQualityIndicatorsCSVPath = XSDataString(dozorCsvPyarchPath) EDPluginISPyBSetImageQualityIndicatorsPlot = self.loadPlugin("EDPluginISPyBSetImageQualityIndicatorsPlotv1_4") EDPluginISPyBSetImageQualityIndicatorsPlot.dataInput = xsDataInputISPyBSetImageQualityIndicatorsPlot EDPluginISPyBSetImageQualityIndicatorsPlot.executeSynchronous() except: self.warning("Couldn't copy files to pyarch: {0}".format(dozorPlotPyarchPath)) self.sendMessageToMXCuBE("Processing finished", "info") self.setStatusToMXCuBE("Success")
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(): 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, 0755) strOutputDirname = tempfile.mkdtemp(prefix="EDPluginPyarchThumbnailv10_", dir=strTmpUser) os.chmod(strOutputDirname, 0755) 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, _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 storeResultsInISPyB(self, _strSubject, _strMessage): strSubject = _strSubject strMessage = _strMessage xsDataResultCharacterisation = self.edPluginControlInterface.getDataOutput().getResultCharacterisation() if self.bIsEigerDetector: xsDataResultCharacterisation = self.makeNumberOfImagesMultipleOf100(xsDataResultCharacterisation) self.xsDataResultMXCuBE.setCharacterisationResult(xsDataResultCharacterisation) xsDataResultControlISPyB = self.edPluginControlInterface.getDataOutput().getResultControlISPyB() if xsDataResultControlISPyB != None: self.xsDataResultMXCuBE.setScreeningId(xsDataResultControlISPyB.getScreeningId()) if xsDataResultCharacterisation != None: self.xsDataResultMXCuBE.characterisationResult = xsDataResultCharacterisation strPathCharacterisationResult = os.path.join(self.getWorkingDirectory(), "CharacterisationResult.xml") xsDataResultCharacterisation.exportToFile(strPathCharacterisationResult) self.xsDataResultMXCuBE.setListOfOutputFiles(XSDataString(strPathCharacterisationResult)) # For the moment, create "DNA" style output directory strPathToDNAFileDirectory = self.createDNAFileDirectoryPath(xsDataResultCharacterisation) xsDataDictionaryLogFile = None if self.createDNAFileDirectory(strPathToDNAFileDirectory): xsDataDictionaryLogFile = self.createOutputFileDictionary( xsDataResultCharacterisation, strPathToDNAFileDirectory ) strPyArchPathToDNAFileDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strPathToDNAFileDirectory) if self.createDNAFileDirectory(strPyArchPathToDNAFileDirectory): xsDataDictionaryLogFile = self.createOutputFileDictionary( xsDataResultCharacterisation, strPyArchPathToDNAFileDirectory ) self.xsDataResultMXCuBE.setOutputFileDictionary(xsDataDictionaryLogFile) if xsDataResultCharacterisation.getStatusMessage(): strMessage += "\n\n" strMessage += xsDataResultCharacterisation.getStatusMessage().getValue() if xsDataResultCharacterisation.getShortSummary(): strMessage += "\n\n" strMessage += xsDataResultCharacterisation.getShortSummary().getValue() self.sendEmail(strSubject, strMessage) # Fix for bug EDNA-55 : If burning strategy EDNA2html shouldn't be run bRunExecOutputHTML = False xsDataInputMXCuBE = self.getDataInput() xsDataDiffractionPlan = xsDataInputMXCuBE.getDiffractionPlan() if xsDataDiffractionPlan is not None and xsDataDiffractionPlan.getStrategyOption() is not None: strStrategyOption = xsDataDiffractionPlan.getStrategyOption().getValue() if strStrategyOption.find("-DamPar") != -1: bRunExecOutputHTML = False if (self.edPluginExecOutputHTML is not None) and bRunExecOutputHTML: self.edPluginExecOutputHTML.setDataInput( XSDataFile(XSDataString(strPathToDNAFileDirectory)), "dnaFileDirectory" ) self.edPluginExecOutputHTML.execute() # Fix for bug MXSUP-251: Put the BEST .par file in the EDNA characterisation root directory xsDataIntegrationResult = xsDataResultCharacterisation.getIntegrationResult() if xsDataIntegrationResult: listXSDataIntegrationSubWedgeResult = xsDataIntegrationResult.getIntegrationSubWedgeResult() for xsDataIntegrationSubWedgeResult in listXSDataIntegrationSubWedgeResult: if xsDataIntegrationSubWedgeResult.getBestfilePar() is not None: strBestfilePar = xsDataIntegrationSubWedgeResult.getBestfilePar().getValue() # Put the file one directory above the mxCuBE v1.3 plugin working directory: strDir = os.path.dirname(self.getWorkingDirectory()) strPath = os.path.join(strDir, "bestfile.par") EDUtilsFile.writeFile(strPath, strBestfilePar) break # Execute plugin which creates a simple HTML page self.executeSimpleHTML(xsDataResultCharacterisation) # Upload the best wilson plot path to ISPyB strBestWilsonPlotPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(xsDataResultCharacterisation) strBestWilsonPlotPyarchPath = None if strBestWilsonPlotPath is not None and strPyArchPathToDNAFileDirectory is not None: # Copy wilson path to Pyarch strBestWilsonPlotPyarchPath = os.path.join( strPyArchPathToDNAFileDirectory, os.path.basename(strBestWilsonPlotPath) ) if not os.path.exists(strBestWilsonPlotPyarchPath): if not os.path.exists(os.path.dirname(strBestWilsonPlotPyarchPath)): os.makedirs(os.path.dirname(strBestWilsonPlotPyarchPath), 755) shutil.copy(strBestWilsonPlotPath, strBestWilsonPlotPyarchPath) self.DEBUG("Best wilson pyarch path: %s " % strBestWilsonPlotPyarchPath) if self.edPluginControlInterface.dataOutput.resultControlISPyB is not None: xsDataInputISPyBSetBestWilsonPlotPath = XSDataInputISPyBSetBestWilsonPlotPath() xsDataInputISPyBSetBestWilsonPlotPath.dataCollectionId = ( self.edPluginControlInterface.dataOutput.resultControlISPyB.dataCollectionId ) xsDataInputISPyBSetBestWilsonPlotPath.bestWilsonPlotPath = XSDataString(strBestWilsonPlotPyarchPath) edPluginSetBestWilsonPlotPath = self.loadPlugin( "EDPluginISPyBSetBestWilsonPlotPathv1_4", "ISPyBSetBestWilsonPlotPath" ) edPluginSetBestWilsonPlotPath.dataInput = xsDataInputISPyBSetBestWilsonPlotPath edPluginSetBestWilsonPlotPath.executeSynchronous() # Only for the ESRF: if EDUtilsPath.isESRF(): # For EXI: create workflow entry with one workflow step self.edPluginStoreWorkflow = self.loadPlugin(self.strPluginStoreWorkflow) self.edPluginStoreWorkflowStep = self.loadPlugin(self.strPluginStoreWorkflowStep) self.edPluginUpdateDataCollectionGroupWorkflowId = self.loadPlugin( self.strUpdateDataCollectionGroupWorkflowId ) xsDataISPyBWorkflow = XSDataISPyBWorkflow() xsDataISPyBWorkflow.workflowType = XSDataString("Characterisation") xsDataISPyBWorkflow.workflowTitle = XSDataString("Characterisation") xsDataInputISPyBStoreWorkflow = XSDataInputISPyBStoreWorkflow() xsDataInputISPyBStoreWorkflow.workflow = xsDataISPyBWorkflow self.edPluginStoreWorkflow.dataInput = xsDataInputISPyBStoreWorkflow self.edPluginStoreWorkflow.executeSynchronous() if ( self.edPluginStoreWorkflow.dataOutput is not None and self.edPluginStoreWorkflow.dataOutput.workflowId is not None ): workflowId = self.edPluginStoreWorkflow.dataOutput.workflowId.value # Update data collection group xsDataInputISPyBUpdateDataCollectionGroupWorkflowId = ( XSDataInputISPyBUpdateDataCollectionGroupWorkflowId() ) xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.workflowId = XSDataInteger(workflowId) xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.fileLocation = XSDataString( os.path.dirname(self.xsDataFirstImage.path.value) ) xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.fileName = XSDataString( os.path.basename(self.xsDataFirstImage.path.value) ) self.edPluginUpdateDataCollectionGroupWorkflowId.dataInput = ( xsDataInputISPyBUpdateDataCollectionGroupWorkflowId ) self.edPluginUpdateDataCollectionGroupWorkflowId.executeSynchronous() xsDataInputISPyBStoreWorkflowStep = XSDataInputISPyBStoreWorkflowStep() xsDataInputISPyBStoreWorkflowStep.workflowId = XSDataInteger(workflowId) xsDataInputISPyBStoreWorkflowStep.workflowStepType = XSDataString("Characterisation") xsDataInputISPyBStoreWorkflowStep.status = XSDataString("Success") if strBestWilsonPlotPyarchPath is not None: xsDataInputISPyBStoreWorkflowStep.imageResultFilePath = XSDataString( strBestWilsonPlotPyarchPath ) xsDataInputISPyBStoreWorkflowStep.htmlResultFilePath = XSDataString(strPyArchPathToDNAFileDirectory) if self.edPluginExecSimpleHTML.dataOutput is not None: strResultFilePath = self.edPluginExecSimpleHTML.dataOutput.pathToJsonFile.path.value # strPyarchResultFilePath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strResultFilePath) xsDataInputISPyBStoreWorkflowStep.resultFilePath = XSDataString(strResultFilePath) self.edPluginStoreWorkflowStep.dataInput = xsDataInputISPyBStoreWorkflowStep self.edPluginStoreWorkflowStep.executeSynchronous()
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)