def buildInput(self, _edObject=None):
"""
This method creates an XSDataInputCharacterisation object depending on the input:
- If dataFile input is provided, uses the "createDataInputCharacterisationFromDataFiles" to retrieve the data collection.
- If dataSet input is provided, uses the "createDataInputCharacterisationFromDataSets" method to retrieve the data collection.
After having retrieved an initial XSDataInputCharacterisation object, it then uses the method "updateDataInputCharacterisation" for
updating certain parameters.
"""
EDVerbose.DEBUG("EDPluginControlCCP4iv1_1.buildInput...")
xsDataInputCCP4i = self.getDataInput()
pyListXSDataFile = xsDataInputCCP4i.getDataFile()
if(len(pyListXSDataFile) > 0):
# Ok, we got data files - assemble these to an XSDataInputCharacterisation object.
xsDataInputCharacterisation = self.createDataInputCharacterisationFromDataFiles(pyListXSDataFile)
else:
# No data file input - check for image files:
pyListXSDataCCP4iDataSet = xsDataInputCCP4i.getDataSet()
if (pyListXSDataCCP4iDataSet is None):
pyStrErrorMessage = "No input data!"
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.buildInput', 'EDPluginControlCCP4iv1_1', pyStrErrorMessage)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
xsDataInputCharacterisation = self.createDataInputCharacterisationFromDataSets(pyListXSDataCCP4iDataSet)
# Update the data collection with other parameters
if (xsDataInputCharacterisation is None):
strError = "EDPluginControlCCP4iv1_1.buildInput: failed when building input."
EDVerbose.ERROR(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
self.updateDataInputCharacterisation(xsDataInputCharacterisation)
return xsDataInputCharacterisation
def compareTwoValues(self, _value1, _value2, _dTolerance=0.000001):
"""
This method compares two values which can be of type double, integer or string.
The types of the two values two be compared must be identical.
If the value is of type double, an optional tolerance can be passed as an
argument to the method. If both values are None the methods returns True.
"""
bReturnValue = False
if (_value1 is None):
if (_value2 is None):
bReturnValue = True
elif (type (_value1) != type(_value2)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginSubWedgeMergev1_1.compareTwoValues', self.getClassName(), "Types of values different : value1=%r, value2=%r" % (type(_value1), type(_value2)))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise Exception, strErrorMessage
elif (type(_value1) == type(0.1)):
if (abs(_value1 - _value2) < _dTolerance):
bReturnValue = True
elif (type(_value1) == type(1)):
if (_value1 == _value2):
bReturnValue = True
elif type(_value1) == type("aaa") or type(_value1) == type(u'unicode'):
if _value1 == _value2:
bReturnValue = True
else:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginSubWedgeMergev1_1.compareTwoValues', self.getClassName(), "Unknown value type : %r for value %r" % (type(_value1), _value1))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise Exception, strErrorMessage
return bReturnValue
def setDataInput(self, _oDataInput, _strDataInputKey=None):
"""
Sets the plugin input data.
_oDataInput could be either an String XML or an XSData object.
"""
EDVerbose.DEBUG("EDPluginWrapperForJobScheduler.setDataInput")
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.getDefaultInputDataKey()
# Allow for None input
if (_oDataInput is None):
EDVerbose.DEBUG("EDPlugin.setDataInput: Data input is None")
self.__dictXMLDataInput[ strDataInputKey ] = []
else:
# Check the type
strXMLDataInput = None
if isinstance(_oDataInput, (str, unicode)):
EDVerbose.DEBUG("EDPlugin.setDataInput: Input Data is string ")
strXMLDataInput = _oDataInput
else:
try:
strXMLDataInput = _oDataInput.marshal()
except BaseException, e:
strErrorMessage = "ERROR: EDPluginWrapperForJobScheduler.setDataInput, cannot marshal data input object"
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Add the object to a list if its key is not the default key
if (strDataInputKey != self.getDefaultInputDataKey()) :
# Check if there's already a list stored
if (not strDataInputKey in self.__dictXMLDataInput.keys()):
self.__dictXMLDataInput[ strDataInputKey ] = []
self.__dictXMLDataInput[ strDataInputKey ].append(strXMLDataInput)
else:
self.__dictXMLDataInput[ strDataInputKey ] = strXMLDataInput
def postProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginExecProcessScript.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginLabelitv10.postProcess...")
strLabelitLog = self.readProcessLogFile()
if (strLabelitLog is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginLabelitv10.postProcess", self.getClassName(), "Could not read the Labelit log file")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
xsDataLabelitScreenOutput = self.parseLabelitScreenOutput(strLabelitLog)
xsDataIntegerSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber()
if (xsDataIntegerSelectedSolutionNumber is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginLabelitv10.postProcess", self.getClassName(), "No selected solution")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
strLabelitMosflmScriptsOutput = self.readProcessFile(self.generateMosflmScriptName(xsDataIntegerSelectedSolutionNumber.getValue()))
xsDataLabelitMosflmScriptsOutput = self.parseMosflmScriptsOutput(strLabelitMosflmScriptsOutput)
xsDataResultLabelit = XSDataResultLabelit()
xsDataResultLabelit.setLabelitScreenOutput(xsDataLabelitScreenOutput)
xsDataResultLabelit.setLabelitMosflmScriptsOutput(xsDataLabelitMosflmScriptsOutput)
self.setDataOutput(xsDataResultLabelit)
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of compatible versions
"""
EDPluginExecProcess.postProcess(self)
EDVerbose.DEBUG("EDPluginExecProcessScript.postProcess")
# Tests the compatibles executable versions
listCompatibleVersions = self.getListOfCompatibleVersions()
if(len(listCompatibleVersions) != 0):
bFound = False
for compatibleVersion in listCompatibleVersions:
bFound = self.findStringInLog(compatibleVersion)
if(bFound == True):
break
if(bFound == False):
strErrorMessage = "Plugin not compatible with %s, compatible versions are: %s" % (self.getStringVersion(), self.getCompatibleVersionsStringLine())
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
def preProcess(self, _edObject=None):
"""
Loads the ISPyB execution plugin and prepares the input data
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlISPyBv1_1.preProcess...")
if (self.hasDataInput("shortComments")):
self.__strShortComments = self.getDataInput("shortComments")[0].getValue()
if (self.hasDataInput("comments")):
self.__strComments = self.getDataInput("comments")[0].getValue()
if (self.hasDataInput("statusMessage")):
self.__strStatusMessage = self.getDataInput("statusMessage")[0].getValue()
self.m_edPluginExecISPyB = self.loadPlugin(self.m_edStringPluginExecISPyBName)
from EDHandlerXSDataISPyBv1_2 import EDHandlerXSDataISPyBv1_2
xsDataInputISPyB = None
xsDataISPyBImage = None
try:
xsDataISPyBScreening = EDHandlerXSDataISPyBv1_2.generateXSDataISPyBScreening(self.getDataInput(), self.__strShortComments, self.__strComments)
xsDataISPyBScreeningInput = EDHandlerXSDataISPyBv1_2.generateXSDataISPyBScreeningInput(self.getDataInput())
xsDataISPyBScreeningOutputContainer = EDHandlerXSDataISPyBv1_2.generateXSDataISPyBScreeningOutputContainer(self.getDataInput(), self.__strStatusMessage)
if (xsDataISPyBScreening.getDataCollectionId() is None):
xsDataISPyBImage = EDHandlerXSDataISPyBv1_2.generateXSDataISPyBImage(self.getDataInput())
except Exception, error:
# This exception handling needs to be rethought, see bug #43.
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlISPyBv1_1.preProcess: Unexpected error in ISPyB handler: ", error)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def createDataInputCharacterisationFromDataFiles(self, _pyListXSDataFile):
"""
This method takes as input a list of paths to XML data files. It parses
these files and create a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG("EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataFiles")
xsDataInputCharacterisation = None
for xsDataInputFile in _pyListXSDataFile:
try:
pyStrInputFileContent = EDUtilsFile.readFile(xsDataInputFile.getPath().getValue())
xsDataInputCharacterisationCurrent = XSDataInputCharacterisation.parseString(pyStrInputFileContent)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (xsDataInputCharacterisationCurrent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', "None data collection")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Instantiate the xsDataInputCharacterisation object if it's not already done.
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataInputCharacterisation.setDataCollection(xsDataInputCharacterisationCurrent.getDataCollection())
def configure(self):
"""
Gets the dbserver parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration is None, using default settings")
else:
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration found, using settings from there")
strDbserverHost = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverHost")
if(strDbserverHost == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverHost(strDbserverHost)
strDbserverPort = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverPort")
if(strDbserverPort == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverPort(int (strDbserverPort))
def setPluginInput(self, _edPlugin):
_edPlugin.setDataInput(XSDataInputXAFSDataBatchProcessing())
xsDataInputSpline = XSDataInputSpline()
if (self.__fRbkg):
xsDataInputSpline.setRbkg(XSDataFloat(self.__fRbkg))
_edPlugin.getDataInput().setSplineDataInput(xsDataInputSpline)
xsDataInputFFTF = XSDataInputFFTF()
if (self.__fftfKmin):
xsDataInputFFTF.setKmin(XSDataFloat(self.__fftfKmin))
if (self.__fftfKmax):
xsDataInputFFTF.setKmax(XSDataFloat(self.__fftfKmax))
if (self.__fftfDk):
xsDataInputFFTF.setDk(XSDataFloat(self.__fftfDk))
if (self.__fftfKweight):
xsDataInputFFTF.setKweight(XSDataFloat(self.__fftfKweight))
_edPlugin.getDataInput().setFftfDataInput(xsDataInputFFTF)
if (not self.__strDatasetFileNames is None):
try:
if (self.__strNxsEnergy and self.__strNxsLnI0It):
_edPlugin.readXAFSNexusFiles(self.__strDatasetFileNames, self.__strNxsEnergy, self.__strNxsLnI0It, self.__strNxsScanIndex)
except Exception:
errorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % ("EDApplicationXAFSBatchProcessing.setPluginInput", self.__strDatasetFileNames)
EDVerbose.error(errorMessage)
raise RuntimeError, errorMessage
def preProcess(self, _edObject=None):
"""
Loads the ISPyB execution plugin and prepares the input data
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlISPyBv1_4.preProcess...")
if (self.hasDataInput("shortComments")):
self.strShortComments = self.getDataInput("shortComments")[0].getValue()
if (self.hasDataInput("comments")):
self.strComments = self.getDataInput("comments")[0].getValue()
if (self.hasDataInput("statusMessage")):
self.strStatusMessage = self.getDataInput("statusMessage")[0].getValue()
self.edPluginExecISPyB = self.loadPlugin(self.edStringPluginExecISPyBName)
try:
xsDataInputISPyBStoreScreening = EDHandlerXSDataISPyBv1_4.generateXSDataInputISPyBStoreScreening(self.getDataInput(),
self.strStatusMessage, \
self.strShortComments, \
self.strComments)
except Exception, error:
raise
# This exception handling needs to be rethought, see bug #43.
errorMessage = "EDPluginControlISPyBv1_4.preProcess: Unexpected error in ISPyB handler: %r" % error
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def buildInput(self, _edPlugin=None):
"""
To be overridden by sub classes. This method should return an XSDataCollection object.
"""
errorMessage = EDMessage.ERROR_ABSTRACT_METHOD_02 % (self.getPluginName(), 'buildInput')
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def preProcess(self, _edObject=None):
"""
The pre-process of ED Plugin Control DiffractionCT Powder Integration consists in preparing the input data for SPD Cake.
and declares the execution plugin as EDPluginFit2DCacke
"""
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlDCTPowderIntegrationv1_1.preProcess")
# Load the execution plugin
self.m_edPluginPowderIntegration = self.loadPlugin(self.m_edStringControlledPluginName)
#Retrive its'datamodel
xsDataInputSPDCake = XSDataInputSPDCake()
instrumentParameters = self.getDataInput().getInstrumentParameters()
imageParameters = self.getDataInput().getImageParameters()
xsDataInputSPDCake.setInputFile(self.getDataInput().getImageFile())
xsDataInputSPDCake.setWavelength(instrumentParameters.get_diffrn_radiation_wavelength())
xsDataInputSPDCake.setSampleToDetectorDistance(instrumentParameters.get_pd_instr_dist_spec_detc())
xsDataInputSPDCake.setAngleOfTilt(imageParameters.get_pd_instr_special_details_tilt_angle())
xsDataInputSPDCake.setTiltRotation(imageParameters.get_pd_instr_special_details_tilt_rotation())
xsDataInputSPDCake.setDarkCurrentImageFile(imageParameters.get_file_correction_image_dark_current())
xsDataInputSPDCake.setFlatFieldImageFile(imageParameters.get_file_correction_image_flat_field())
xsDataInputSPDCake.setSpatialDistortionFile(imageParameters.get_file_correction_spline_spatial_distortion())
# EDVerbose.screen("imageParameters.get_array_element_size_1: %s" % imageParameters.get_array_element_size_1().marshal())
xsDataInputSPDCake.setBeamCentreInPixelsX(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_1()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_1())))
xsDataInputSPDCake.setBeamCentreInPixelsY(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_2()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_2())))
xsDataInputSPDCake.setPixelSizeX(imageParameters.get_array_element_size_1())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setPixelSizeY(imageParameters.get_array_element_size_2())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setBufferSizeX(XSDataInteger(2048))
xsDataInputSPDCake.setBufferSizeY(XSDataInteger(2048))
xsDataInputSPDCake.setStartAzimuth(XSDataAngle(0))
xsDataInputSPDCake.setStopAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setStepAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setOutputDirCake(self.getDataInput().getDestinationDir())
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(True))
try:
self.m_edPluginPowderIntegration.setDataInput(xsDataInputSPDCake)
except Exception, error:
# This exception handling needs to be rethought, see bug #43.
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlDCTPowderIntegrationv1_1.preProcess: Unexpected error in SPD handler: ", error)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def connect(self, _pyClassMethod):
"""
Connects a signal between an object and a method in an other object.
"""
if (_pyClassMethod == None):
EDVerbose.error("EDSlot.connect: None class method")
return
self.synchronizeOn() # Block the thread
self.__listMethod.append(_pyClassMethod)
self.synchronizeOff() # Release the thread
def processCommandLineInputFilePath(self):
"""
"""
EDVerbose.DEBUG("EDApplication.processCommandLineInputFilePath")
if (not self.__edCommandLine.existCommand(EDApplication.DATASET_PARAM_LABEL)):
EDVerbose.error("No %s command line argument found!" % EDApplication.DATASET_PARAM_LABEL)
self.__bIsFailure = True
else:
self.__strDataInputFilePath = self.getCommandLineArgument(EDApplication.DATASET_PARAM_LABEL)
EDVerbose.DEBUG("EDApplication.initApplication : %s = %s" % (EDApplication.DATASET_PARAM_LABEL, self.__strDataInputFilePath))
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginEDFReadHeaderv1_0.preProcess")
# Check that the input file is present
edStringPathToInputFile = self.getDataInput().getEdfFile().getPath().getValue()
if (not os.path.exists(edStringPathToInputFile)):
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", edStringPathToInputFile)
EDVerbose.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
def kill(self):
EDVerbose.WARNING("I will kill subprocess %s pid= %s" % (self.__subprocess, self.__iPID))
EDUtilsPlatform.kill(self.__iPID)
self.synchronizeOff()
self.__strExecutionStatus = "timeout"
EDVerbose.DEBUG("EDPluginExecProcess.process ========================================= ERROR! ================")
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginExecProcess.process', self.getClassName(), "Timeout ")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def processCommandLinePluginName(self):
"""
"""
EDVerbose.DEBUG("EDApplication.processCommandLinePluginName")
if (not self.__edCommandLine.existCommand(EDApplication.PLUGIN_PARAM_LABEL)):
EDVerbose.error("No %s command line argument found!" % EDApplication.PLUGIN_PARAM_LABEL)
self.__bIsFailure = True
else:
self.__strPluginName = self.getCommandLineArgument(EDApplication.PLUGIN_PARAM_LABEL)
EDVerbose.DEBUG("EDApplication.processCommandLinePluginName : %s = %s" % (EDApplication.PLUGIN_PARAM_LABEL, self.__strPluginName))
def processCommandLineItems(self, _strCommandLineItem):
if(_strCommandLineItem == EDApplicationDimplev0.TEMPLATE_PARAM_LABEL):
self.bTemplateMode = True
self.strGeneratedTemplateFile = self.getCommandLineArgument(EDApplicationDimplev0.TEMPLATE_PARAM_LABEL)
if (self.strGeneratedTemplateFile == None):
strErrorMessage = EDMessage.ERROR_MANDATORY_PARAM_MISSING_02 % ("EDApplicationDimplev0.processCommandLineItems", "No argument for command line %s key word found!" % \
EDApplicationDimplev0.TEMPLATE_PARAM_LABEL)
EDVerbose.error(strErrorMessage)
return False
if (not os.path.isabs(self.strGeneratedTemplateFile)):
self.strGeneratedTemplateFile = os.path.abspath(os.path.join(self.getCurrentWorkingDirectory(), self.strGeneratedTemplateFile))
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginCopyExifv1_0.preProcess")
self.strInfile = self.getDataInput().getInputImagePath().getPath().getValue()
self.strOutfile = self.getDataInput().getOutputImagePath().getPath().getValue()
for oneFile in [self.strInfile, self.strOutfile]:
if not os.path.isfile(oneFile):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", oneFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def doSuccessWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlID29CreateThumbnailv1_0.doSuccessWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID29CreateThumbnailv1_0.doSuccessWaitFile")
# Check that the image is really there
# The image is here - make the first thumbnail
if not self.__edPluginWaitFile.getDataOutput().getTimedOut().getValue():
self.__edPluginExecThumbnail.connectSUCCESS(self.doSuccessExecThumbnail)
self.__edPluginExecThumbnail.connectFAILURE(self.doFailureExecThumbnail)
self.__edPluginExecThumbnail.executeSynchronous()
else:
EDVerbose.error("Time-out while waiting for image!")
self.setFailure()
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
strError = self.readProcessErrorLogFile()
if((strError is not None) and (strError != "")):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginBestv1_1.postProcess', 'EDPluginBestv1_1', strError)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
outputData = self.getOutputDataFromDNATableFile(os.path.join(self.getWorkingDirectory(), self.getScriptBaseName() + "_dnaTables.xml"))
self.setDataOutput(outputData)
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginSPDCakev1_0.preProcess")
# Check that the input data and correction images are present
xsDataInputSPDCake = self.getDataInput()
pathToInputFile = xsDataInputSPDCake.getInputFile().getPath().getValue()
if (not os.path.exists(pathToInputFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToInputFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToDarkCurrentImageFile = xsDataInputSPDCake.getDarkCurrentImageFile().getPath().getValue()
if (not os.path.exists(pathToDarkCurrentImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToDarkCurrentImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToFlatFieldImageFile = xsDataInputSPDCake.getFlatFieldImageFile().getPath().getValue()
if (not os.path.exists(pathToFlatFieldImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToFlatFieldImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pathToSpatialDistortionFile = xsDataInputSPDCake.getSpatialDistortionFile().getPath().getValue()
if (not os.path.exists(pathToSpatialDistortionFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pathToSpatialDistortionFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if xsDataInputSPDCake.getOutputDir() is not None:
self.outputDir = xsDataInputSPDCake.getOutputDir().getPath().getValue()
if not os.path.isdir(self.outputDir):
os.makedirs(self.outputDir)
self.generateSPDCommand()
def getReferenceDataOutputFile(self, _strDataOutputKey=None):
"""
Returns the data input file
"""
strReferenceDataOutputFile = None
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self._strDefaultOutputDataKey
if (strDataOutputKey in self._dictStrReferenceDataOutputFiles.keys()):
strReferenceDataOutputFile = self._dictStrReferenceDataOutputFiles[ strDataOutputKey ]
else:
strErrorMessage = "ERROR: " + str(self.__class__) + ".getReferenceDataOutputFile, no data output file defined for key: " + strDataOutputKey
EDVerbose.error(strErrorMessage)
raise RuntimeError, strErrorMessage
return strReferenceDataOutputFile
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("EDPluginExecSaxsAddMetadatav1_0.preProcess")
self.strImage = self.getDataInput().getInputImage().getPath().getValue()
if not os.path.isfile(self.strImage):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", self.strImage)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if self.getDataInput().getKey() is not None:
self.strKey = self.getDataInput().getKey().getValue()
if self.getDataInput().getValue() is not None:
self.strValue = self.getDataInput().getValue().getValue()
self.generateEdfheaderaddkey2DCommands()
def configure(self):
EDPluginExecProcessScript.configure(self)
EDVerbose.DEBUG("EDPluginControlLabelitv10.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginControlLabelitv10.configure: No Labelit plugin item defined.")
xsPluginItem = XSPluginItem()
strPathToLabelitSetpathScript = EDConfiguration.getStringParamValue(xsPluginItem, self.strCONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
if(strPathToLabelitSetpathScript == None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlLabelitv10.configure', self.getClassName(), "Configuration parameter missing: " + self.strCONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
self.setPathToLabelitSetpathScript(strPathToLabelitSetpathScript)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
strError = self.readProcessErrorLogFile()
if((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginMxv1ParamsToXMLv1_0.postProcess', 'EDPluginMxv1ParamsToXMLv1_0', strError)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# This should work as long as there is a single output, i.e. not a list:
strFilePath = os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
xsDataFileResult = XSDataFile()
xsDataFileResult.setPath(XSDataString(strFilePath))
# Do not specify name of output here:
self.setDataOutput(xsDataFileResult)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
EDVerbose.DEBUG("EDPluginBestv1_2.finallyProcess")
strError = self.readProcessErrorLogFile()
if((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginBestv1_2.postProcess', 'EDPluginBestv1_2', strError)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setDataOutput(XSDataResultBest())
self.setFailure()
else:
xsDataResultBest = self.getOutputDataFromDNATableFile(EDUtilsPath.mergePath(self.getWorkingDirectory(), self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
self.setDataOutput(xsDataResultBest)
def createPlugin(self):
"""
Creates a plugin instance
"""
edPlugin = None
exceptionObject = None
try:
edFactoryPlugin = EDFactoryPlugin()
edPlugin = edFactoryPlugin.loadPlugin(self.getPluginName())
except ImportError(exceptionObject):
strWarningMessage = "Could not create the plugin: %s, reason: %s" % (self.getPluginName(), exceptionObject)
EDVerbose.WARNING(strWarningMessage)
if edPlugin is None:
if exceptionObject is None:
EDVerbose.error("EDTestCasePlugin.createPlugin: Could not create plugin: " + self.getPluginName())
return edPlugin
def getXSDataResultCharacterisation(self, _strListOfOutputFiles):
listResult = _strListOfOutputFiles.split()
# Search for the outputfile
xsDataResultCharacterisation = None
strPathToXSDataResultCharacteristion = None
for strLine in listResult:
if (strLine.find("dataOutput.xml") != -1):
strPathToXSDataResultCharacteristion = strLine
if (strPathToXSDataResultCharacteristion is not None):
xsDataResultCharacterisation = XSDataResultCharacterisation.parseFile(strPathToXSDataResultCharacteristion)
else:
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlInterfaceToMXCuBEv1_2.getXSDataResultCharacterisation", "Cannot find dataOutput.xml file in %s" % _strListOfOutputFiles)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
return xsDataResultCharacterisation
def postProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginLabelitv1_1.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginLabelitDistlv1_1.postProcess")
strLabelitDistlLog = self.readProcessLogFile()
if (strLabelitDistlLog is None):
strErrorMessage = "EDPluginLabelitDistlv1_1.postProcess : Could not read the Labelit log file"
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataImageQualityIndicators = self.parseLabelitDistlOutput(strLabelitDistlLog)
xsDataImage = self.getDataInput("referenceImage")[0]
xsDataImageQualityIndicators.setImage(xsDataImage)
self.setDataOutput(xsDataImageQualityIndicators, "imageQualityIndicators")
class EDPluginControlKappaStrategyv2_0(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.strSymopHome = _strSymopHome
def getSymopHome(self):
return self.strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d"
% dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(dSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictMARCCDHeader = self.readHeaderMarccd(strPath)
if (dictMARCCDHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = int(dictMARCCDHeader["nslow"])
iNoPixelsY = int(dictMARCCDHeader["nfast"])
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
fPixelSizeX = float(dictMARCCDHeader["pixelsize_x"]) / 1000.0
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(dictMARCCDHeader["pixelsize_y"]) / 1000.0
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
fBeamPositionX = float(dictMARCCDHeader["beam_x"]) / 1000.0
fBeamPositionY = float(dictMARCCDHeader["beam_y"]) / 1000.0
# Fix for bug 397 - check if the beam position is close to the centre of the image
fTwoTheta = float(dictMARCCDHeader["end_twotheta"]) / 1000.0
xsDataDetector.setTwoTheta(XSDataAngle(fTwoTheta))
if (abs(fTwoTheta) < 0.1):
if (abs(fBeamPositionX /
(fPixelSizeX / 1000.0) - iNoPixelsX / 2.0) >
(2 * iNoPixelsX)):
fBeamPositionX = fBeamPositionX * fPixelSizeX / 1000.0
fBeamPositionY = fBeamPositionY * fPixelSizeY / 1000.0
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictMARCCDHeader["xtal_to_detector"]) / 1000.0
if (abs(fDistance) < 0.1):
fDistanceStart = float(
dictMARCCDHeader["start_xtal_to_detector"]) / 1000.0
fDistanceEnd = float(
dictMARCCDHeader["end_xtal_to_detector"]) / 1000.0
if (abs(fDistanceStart - fDistanceEnd) < 0.1):
fDistance = fDistanceStart
else:
# Somethings very wrong with the distances...
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Inconsistency in MAR CCD image header: start_xtal_to_detector = %d, end_xtal_to_detector = %d" % \
(fDistanceStart, fDistanceEnd)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataDetector.setDistance(XSDataLength(fDistance))
xsDataDetector.setNumberBytesInHeader(
XSDataInteger(float(dictMARCCDHeader["header_size"])))
#xsDataDetector.setSerialNumber( XSDataInteger( dictMARCCDHeader[ "DETECTOR_SN" ] ) ) )
#xsDataDetector.setBin( XSDataString( dictMARCCDHeader[ "BIN" ] ) ) )
#xsDataDetector.setDataType( XSDataString( dictMARCCDHeader[ "TYPE" ] ) ) )
#xsDataDetector.setByteOrder( XSDataString( dictMARCCDHeader[ "BYTE_ORDER" ] ) ) )
xsDataDetector.setImageSaturation(
XSDataInteger(int(dictMARCCDHeader["saturation_level"])))
# Determine type of detector...
if (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("MAR CCD 165"))
xsDataDetector.setType(XSDataString("mar165"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("MAR CCD 225"))
xsDataDetector.setType(XSDataString("mar225"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("MAR CCD 325"))
xsDataDetector.setType(XSDataString("mar325"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % (
"EDPluginExecReadImageHeaderMARCCDv10.process",
"Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(
XSDataWavelength(
float(dictMARCCDHeader["source_wavelength"]) / 100000.0))
xsDataBeam.setExposureTime(
XSDataTime(float(dictMARCCDHeader["exposure_time"]) / 1000.0))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictMARCCDHeader["start_phi"]) / 1000.0
fOscillationWidth = float(
dictMARCCDHeader["rotation_range"]) / 1000.0
xsDataGoniostat.setRotationAxisStart(
XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(
XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
strTimeStamp = dictMARCCDHeader["acquire_timestamp"]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv10.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv10.preProcess',
"No symmetry operators found for Space Group: ",
strSpaceGroup)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
xsDataChemicalComposition = self.__xsDataSampleCopy.getChemicalComposition(
)
if (xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self.__xsDataSampleCopy, iNumOperators)
self.__xsDataSampleCopy.setChemicalComposition(
xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(
def preProcess(self, _edObject=None):
EDPluginExecProcessScript.preProcess(self)
EDVerbose.DEBUG("*** EDPluginFIT2DCakev1_1.preProcess")
# Check that the input data and correction images are present
xsDataInputFIT2DCake = self.getDataInput()
pyStrPathToInputFile = xsDataInputFIT2DCake.getInputFile().getPath().getValue()
if (not os.path.exists(pyStrPathToInputFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pyStrPathToInputFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToDarkCurrentImageFile = xsDataInputFIT2DCake.getDarkCurrentImageFile().getPath().getValue()
if (not os.path.exists(pyStrPathToDarkCurrentImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pyStrPathToDarkCurrentImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToFlatFieldImageFile = xsDataInputFIT2DCake.getFlatFieldImageFile().getPath().getValue()
if (not os.path.exists(pyStrPathToFlatFieldImageFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pyStrPathToFlatFieldImageFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
pyStrPathToSpatialDistortionFile = xsDataInputFIT2DCake.getSpatialDistortionFile().getPath().getValue()
if (not os.path.exists(pyStrPathToSpatialDistortionFile)):
strErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (self.getPluginName() + ".preProcess", pyStrPathToSpatialDistortionFile)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Rev 946
##Generate the image cleaned from the background and flatfield
# edfImage=EDF.EdfFile(pyStrPathToInputFile)
# npArrayImage=edfImage.GetData(0).astype("float32")
# edfDark=EDF.EdfFile(pyStrPathToDarkCurrentImageFile)
# Md=edfDark.GetData(0).astype("float32")
# edfFlat=EDF.EdfFile( pyStrPathToFlatFieldImageFile )
# Mf=edfFlat.GetData(0).astype("float32")
# npaTmp = NP.zeros_like(npArrayImage)
# npaNum = NP.maximum(npArrayImage-Md,NP.zeros_like(npArrayImage))
# npaDen = NP.maximum(Mf-Md,NP.ones_like(npArrayImage))
# npaTmp += NP.max( npaDen )
# npaRes = npaTmp * npaNum / npaDen
#
# edfOutfile=EDF.EdfFile(os.path.join( self.getWorkingDirectory(), "CleanedImage.edf") )
# edfOutfile.WriteImage(edfImage.GetHeader(0), npaRes.astype("uint16"), Append=0)
##End Generate cleaned image
#Generate the image cleaned from the background and flatfield
edfImage = EDF.EdfFile(pyStrPathToInputFile)
npArrayImage = edfImage.GetData(0).astype("float32")
edfDark = EDF.EdfFile(pyStrPathToDarkCurrentImageFile)
Md = edfDark.GetData(0).astype("float32")
edfFlat = EDF.EdfFile(pyStrPathToFlatFieldImageFile)
Mf = edfFlat.GetData(0).astype("float32")
#npaTmp = NP.zeros_like(npArrayImage)
npaNum = npArrayImage - Md
npaDen = Mf
# npaTmp += NP.max( npaDen )
npaRes = npaNum / npaDen
edfOutfile = EDF.EdfFile(os.path.join(self.getWorkingDirectory(), "CleanedImage.edf"))
edfOutfile.WriteImage(edfImage.GetHeader(0), npaRes.astype("float32"), Append=0)
#End Generate cleaned image
self.generateFIT2DCommands()
numpy = EDFactoryPluginStatic.preImport("numpy",
numpyPath,
_strMethodVersion="__version__")
h5py = EDFactoryPluginStatic.preImport("h5py",
h5pyPath,
_strMethodVersion="version.api_version",
_strForceVersion="1.8")
Image = EDFactoryPluginStatic.preImport("Image",
imagingPath,
_strMethodVersion="VERSION")
fabio = EDFactoryPluginStatic.preImport("fabio",
fabioPath,
_strMethodVersion="version")
if h5py is None:
EDVerbose.error("h5py is None ... please investigate why !!!")
EDVerbose.writeErrorTrace()
# raise ImportError("EDPluginHDF5 cannot work without h5py !!!")
if "EDNA_SITE" not in os.environ:
os.environ["EDNA_SITE"] = "edna-site"
class EDPluginHDF5(EDPlugin):
"""
This is a common part for all EDNA plugin writing HDF5. most methods are class methods
"""
__semCls = Semaphore()
__dictHDF5 = {} #key: filename, value: hdf5 h5py objects
__dictLock = {} #key: filename, value:semaphores for writing
__bConfigured = False
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " + self._strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
bSpaceGroupForced = True
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def preProcess(self):
"""
Creates the application working directory (log dir)
Initializes the configuration
retrieves the plugin xml data to be passed to the plugin
"""
EDVerbose.DEBUG("EDApplication.preProcess")
self.processCommandline()
if (not self.__bIsFailure):
# Check that the plugin can be located
strPluginLocation = EDFactoryPluginStatic.getFactoryPlugin(
).getModuleLocation(self.__strPluginName)
if (strPluginLocation is None):
EDVerbose.error("Plugin %s cannot be loaded!" %
self.__strPluginName)
self.__bIsFailure = True
# Check that the input file can be read
if (self.getDataInputFilePath() is not None) and (
not os.path.exists(self.__strDataInputFilePath)):
EDVerbose.error("Input XML file not found : %s" %
self.__strDataInputFilePath)
self.__bIsFailure = True
# Check that the output file can be created
if (self.__strDataOutputFilePath is not None):
strOutputDirectory = os.path.dirname(
self.__strDataOutputFilePath)
if (strOutputDirectory is None or strOutputDirectory == ""):
strOutputDirectory = os.getcwd()
self.__strDataOutputFilePath = os.path.join(
strOutputDirectory, self.__strDataOutputFilePath)
if (not os.access(strOutputDirectory, os.W_OK)):
EDVerbose.error("Output directory not writable: %s" %
strOutputDirectory)
self.__bIsFailure = True
elif (os.path.exists(self.__strDataOutputFilePath)):
if (not os.access(self.__strDataOutputFilePath, os.W_OK)):
EDVerbose.error("Output file not writable: %s" %
self.__strDataOutputFilePath)
self.__bIsFailure = True
if (not self.__bIsFailure):
EDVerbose.DEBUG("EDApplication.PLUGIN_PARAM_LABEL: " +
EDApplication.PLUGIN_PARAM_LABEL)
if self.__strConfigurationFileName is not None:
# Load the configuration file
if (os.path.exists(self.__strConfigurationFileName)):
EDVerbose.screen("Loading Configuration file: %s" %
self.__strConfigurationFileName)
EDConfigurationStatic.addConfigurationFile(
self.__strConfigurationFileName, _bReplace=True)
else:
EDVerbose.warning("Cannot find configuration file: %s" %
self.__strConfigurationFileName)
pyDictionary = {}
pyDictionary["${EDNA_HOME}"] = EDUtilsPath.getEdnaHome()
if self.getDataInputFilePath() is not None:
self.__strXMLData = EDUtilsFile.readFileAndParseVariables(
self.getDataInputFilePath(), pyDictionary)
# Create the application working directory
if (self.__strWorkingDir is None):
self.__strWorkingDir = self.__strApplicationInstanceName
self.createApplicationWorkingDirectory()
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus6Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictPilatus6MHeader = self.readHeaderPilatus6M(strPath)
if (dictPilatus6MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderPilatus6Mv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 2463
iNoPixelsY = 2527
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictPilatus6MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictPilatus6MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split()
fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX
fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictPilatus6MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictPilatus6MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictPilatus6MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictPilatus6MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictPilatus6MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictPilatus6MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictPilatus6MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("PILATUS 6M"))
xsDataDetector.setType(XSDataString("pilatus6m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictPilatus6MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictPilatus6MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictPilatus6MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictPilatus6MHeader[ "Angle_increment" ].split(" ")[0])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
#
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
if "DateTime" in dictPilatus6MHeader:
strTimeStamp = dictPilatus6MHeader[ "DateTime" ]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
def set(self, value=0, filename="test.edf", position=(0, 0)):
"""
This is the set method that will first ensure that the data are available
#then set a lock on it and finally #No more
write the data
#before unlocking. #No more
@param: value value of the pixel to set
@type value: probably float but can be any figure
@param filename: name of the file to be processed
@type filename: string
@param position: the position of the pixel to modify
@type position: 2-tuple of integers
"""
if not isinstance(value, float):
EDVerbose.error("ERROR The value %s is not a float" % value)
raise Exception("ERROR The value %s is not a float" % value)
if not (isinstance(filename, str) or isinstance(filename, unicode)):
EDVerbose.error("ERROR The filename variable %s is not a string " %
filename)
raise Exception("ERROR The filename variable %s is not a string " %
filename)
if not isinstance(position, tuple):
EDVerbose.error("ERROR The position variable %s is not a tuple " %
position)
raise Exception("ERROR The position variable %s is not a tuple " %
position)
if len(position) != 2:
EDVerbose.error("ERROR in the size of the position-tuple")
raise Exception("ERROR in the size of the position-tuple")
if position[0] < 0:
EDVerbose.error("ERROR in the X part of the position-tuple")
raise Exception("ERROR in the X part of the position-tuple")
if position[1] < 0:
EDVerbose.error("ERROR in the Y part of the position-tuple")
raise Exception("ERROR in the Y part of the position-tuple")
if not self.data.has_key(filename):
EDVerbose.warning(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
pystrDirname, pystrFilename = os.path.split(filename)
fileInDir = []
for onefile in os.listdir(pystrDirname):
if onefile.find("%sSize" % pystrFilename) == 0:
if onefile[-4:].lower() == ".edf":
XxY = onefile.split("Size")[-1][:-4]
try:
size = tuple(
[int(i) for i in tuple(XxY.split("x"))])
except Exception:
size = None
if size:
fileInDir.append(onefile)
if len(fileInDir) > 1:
EDVerbose.warning(
"ERROR, for %s, I found too many images corresponding to what you are looking for : %s"
% (filename, fileInDir))
raise Exception(
"ERROR, I found too many images corresponding to what you are looking for : %s"
% (filename, fileInDir))
elif len(fileInDir) == 1:
EDVerbose.warning(
"WARNING, As The file %s exists, I will try to read it. The expected size is %s"
% (filename, size))
self.size[filename] = size
fullFilename = "%sSize%ix%i.edf" % ((filename, ) + size)
self.headers[filename] = {}
self.data[filename] = numpy.zeros(size, dtype="float32")
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.headers[filename] = self.edf[filename].GetHeader(0)
self.data[filename] = self.edf[filename].GetData(0)
except Exception:
EDVerbose.warning(
"ERROR in reading file %s: Reintializing it" %
filename)
self.edf[filename] = EdfFile(fullFilename)
self.data[filename] = numpy.zeros(size, dtype="float32")
self.headers[filename] = {}
self.synchronizeOff()
if self.data[filename].shape != size:
self.data[filename] = numpy.zeros(size, dtype="float32")
self.headers[filename] = {}
else:
EDVerbose.error(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
raise Exception(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
if position[0] > self.data[filename].shape[0]:
EDVerbose.error(
"ERROR in the X part of the position-tuple: too large %i > %i"
% (position[0], npArray.shape[0]))
raise Exception(
"ERROR in the X part of the position-tuple: too large %i > %i"
% (position[0], npArray.shape[0]))
if position[1] > self.data[filename].shape[1]:
EDVerbose.error(
"ERROR in the Y part of the position-tuple: too large %i > %i"
% (position[1], npArray.shape[1]))
raise Exception(
"ERROR in the Y part of the position-tuple: too large %i > %i"
% (position[1], npArray.shape[1]))
self.data[filename][position[0], position[1]] = value
self.synchronizeOn()
try:
self.edf[filename].WriteImage(self.headers[filename],
self.data[filename],
Append=0)
except Exception:
EDVerbose.error("ERROR in writing image %s at position %s" %
(filename, position))
self.synchronizeOff()
class EDPluginControlStrategyv1_2(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self._strPluginRaddoseName = "EDPluginRaddosev10"
self._edPluginRaddose = None
self._edHandlerXSDataRaddose = None
self._strPluginBestName = "EDPluginBestv1_2"
self._edPluginBest = None
self._edHandlerXSDataBest = None
self._strPluginPlotGleName = "EDPluginExecPlotGlev1_0"
self._edPluginPlotGle = None
self._strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self._strSymopHome = None
self._xsDataSampleCopy = None
# For default chemical composition
self._fAverageAminoAcidVolume = 135.49
self._fAverageCrystalSolventContent = 0.47
self._fAverageSulfurContentPerAminoacid = 0.05
self._fAverageSulfurConcentration = 314
# This varaible determines if Raddose should be executed or not
self._bEstimateRadiationDamage = None
# Raddose log file
self.xsDataFileRaddoseLog = None
def setSymopHome(self, _strSymopHome):
self._strSymopHome = _strSymopHome
def getSymopHome(self):
return self._strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " + self._strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
bSpaceGroupForced = True
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "No symmetry operators found for Space Group: ", strNumOperators)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition()
if(xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(self._xsDataSampleCopy, iNumOperators)
self._xsDataSampleCopy.setChemicalComposition(xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(xsDataChemicalComposition)
self._xsDataSampleCopy.setChemicalComposition(xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput().getExperimentalCondition().getBeam()
# Calculate number of images (MXSUP-1616):
iNumberOfImages = None
xsDataCollection = self.dataInput.dataCollection
if xsDataCollection is not None:
iNumberOfImages = 0
for xsDataSubWedge in xsDataCollection.subWedge:
xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
iOscStart = xsDataGoniostat.rotationAxisStart.value
iOscEnd = xsDataGoniostat.rotationAxisEnd.value
iOscWidth = xsDataGoniostat.oscillationWidth.value
iNumberOfImages += int((iOscEnd-iOscStart)/iOscWidth)
if iNumberOfImages is None:
iNumberOfImages = 1
self.WARNING("No goniostat information, number of images for RADDOSE set to 1")
xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(xsDataBeam, self._xsDataSampleCopy, iNumOperators, iNumberOfImages)
if xsDataRaddoseInput is not None:
self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
self._edPluginRaddose.setBaseDirectory(self.getWorkingDirectory())
self._edPluginRaddose.setBaseName(self._strPluginRaddoseName)
"""
edTestSuite = None
exceptionObject = None
try:
edTestSuite = EDUtilsTest.getFactoryPluginTest().loadPlugin(
_strTestSuiteName)
except ImportError, exceptionObject:
strWarningMessage = "Could not create the test suite: %s, reason: %s" % (
_strTestSuiteName, exceptionObject)
EDVerbose.WARNING(strWarningMessage)
self.__dictTestCaseNotExecuted[_strTestSuiteName] = "%s : %s" % (
self.getClassName(), strWarningMessage)
if edTestSuite is None:
if exceptionObject is None:
EDVerbose.error(
"EDTestSuitePluginUnit.addTestSuiteFromName: Could not create test suite: "
+ _strTestSuiteName)
self.__dictTestSuiteNotExecuted[
_strTestSuiteName] = "%s : Could not create the test suite" % self.getClassName(
)
else:
self.__listTestSuite.append(edTestSuite)
def processKernel(self):
"""
This method executes the test suite.
"""
EDVerbose.DEBUG("Execution: EDTestSuite.processKernel()")
EDVerbose.screen("")
EDVerbose.screen("")
EDVerbose.unitTest(
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG(
"EDPluginControlPyarchThumbnailGeneratorv1_0.preProcess")
# Check that the input image exists and is of the expected type
strPathToDiffractionImage = self.getDataInput().getDiffractionImage(
).getPath().getValue()
strImageFileNameExtension = os.path.splitext(
strPathToDiffractionImage)[1]
if not strImageFileNameExtension in [
".img", ".marccd", ".mccd", ".cbf"
]:
EDVerbose.error(
"Unknown image file name extension for pyarch thumbnail generator: %s"
% strPathToDiffractionImage)
self.setFailure()
else:
# Load the waitFile plugin
xsDataInputWaitFile = XSDataInputWaitFile()
xsDataInputWaitFile.setExpectedSize(
XSDataInteger(self.iExpectedSize))
xsDataInputWaitFile.setExpectedFile(
self.getDataInput().getDiffractionImage())
if self.getDataInput().getWaitForFileTimeOut():
xsDataInputWaitFile.setTimeOut(
self.getDataInput().getWaitForFileTimeOut())
self.edPluginWaitFile = EDPluginWaitFile()
self.edPluginWaitFile.setDataInput(xsDataInputWaitFile)
# Load the execution plugin
self.edPluginExecThumbnail = self.loadPlugin(
self.strExecThumbnailPluginName)
xsDataInputExecThumbnail = XSDataInputExecThumbnail()
xsDataInputExecThumbnail.setInputImagePath(
self.getDataInput().getDiffractionImage())
xsDataInputExecThumbnail.setLevelsInvert(XSDataBoolean(True))
xsDataInputExecThumbnail.setLevelsMin(XSDataDoubleWithUnit(0.0))
xsDataDoubleWithUnitLevelsMax = XSDataDoubleWithUnit(99.95)
xsDataDoubleWithUnitLevelsMax.setUnit(XSDataString("%"))
xsDataInputExecThumbnail.setLevelsMax(
xsDataDoubleWithUnitLevelsMax)
xsDataInputExecThumbnail.setFilterDilatation([XSDataInteger(4)])
xsDataInputExecThumbnail.setLevelsColorize(XSDataBoolean(False))
xsDataInputExecThumbnail.setThumbHeight(XSDataInteger(1024))
xsDataInputExecThumbnail.setThumbWidth(XSDataInteger(1024))
xsDataInputExecThumbnail.setKeepRatio(XSDataBoolean(False))
# 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):
EDVerbose.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 BaseException, e:
EDVerbose.WARNING(
"Couldn't create the directory %s" %
strOutputDirname)
elif os.access(strOutputDirname, os.W_OK):
bIsOk = True
if not bIsOk:
EDVerbose.warning("Cannot write to pyarch directory: %s" %
strOutputDirname)
strOutputDirname = tempfile.mkdtemp(
"", "EDPluginPyarchThumbnailv10_", "/tmp")
EDVerbose.warning("Writing thumbnail images to: %s" %
strOutputDirname)
self.strOutputPathWithoutExtension = os.path.join(
strOutputDirname, strImageNameWithoutExt)
self.strOutputPath = os.path.join(
self.strOutputPathWithoutExtension + ".jpeg")
xsDataInputExecThumbnail.setOutputPath(
XSDataFile(XSDataString(self.strOutputPath)))
self.edPluginExecThumbnail.setDataInput(xsDataInputExecThumbnail)
class EDTestCasePlugin(EDTestCase):
"""
This is the main test class to test a plugin (Unit and Execution)
"""
URL_EDNA_SITE = "http://www.edna-site.org/data/tests/images"
def __init__(self, _strPluginName, _strPluginDir=None, _strTestName=None):
"""
Initialize the test case by determining the paths to the plugin home and plugin test directories.
"""
EDTestCase.__init__(self, _strTestName)
self._edPlugin = None
self._strPluginName = _strPluginName
self._strPluginHome = EDUtilsTest.getFactoryPluginTest().getModuleLocation(_strPluginName)
self._strPluginTestsDataHome = EDUtilsTest.getPluginTestDataDirectory(self.getClassName())
self._listRequiredConfigurationPluginNames = []
self._strConfigurationFile = None
self._oldConfig = None
def preProcess(self):
# Check if the plugin to be tested requires configuration
edPlugin = self.createPlugin()
if edPlugin is None:
strErr = "Unable to create plugin %s: Check the corresponding module" % self.getPluginName()
EDVerbose.ERROR(strErr)
raise RuntimeError(strErr)
if edPlugin.isRequiredToHaveConfiguration():
self._listRequiredConfigurationPluginNames.append(self.getPluginName())
# Check if the required plugin parameters are available
for strPluginName in self._listRequiredConfigurationPluginNames:
if self.getPluginConfiguration(strPluginName) is None:
EDVerbose.DEBUG("EDTestCasePlugin.preProcess: plugin configuration NOT found for plugin %s" % strPluginName)
self.setReasonForNotBeingExectuted("Missing configuration for %s" % strPluginName)
else:
EDVerbose.DEBUG("EDTestCasePlugin.preProcess: plugin configuration found for plugin %s" % strPluginName)
def postProcess(self):
EDTestCase.postProcess(self)
EDConfigurationStatic.setXSConfigurationItem(self._oldConfig)
def getPluginConfiguration(self, _strPluginName=None):
# Load the configuration file if provided
if _strPluginName is None:
strPluginName = self.getPluginName()
else:
strPluginName = _strPluginName
self._oldConfig = EDConfigurationStatic.getXSConfigurationItem(strPluginName)
if self._strConfigurationFile is not None:
edConfig = EDConfiguration(self._strConfigurationFile)
EDConfigurationStatic.setXSConfigurationItem(edConfig.getXSConfigurationItem(strPluginName))
xsConfiguration = EDConfigurationStatic.getXSConfigurationItem(strPluginName)
return xsConfiguration
def setConfigurationFile(self, _strConfigurationFile):
"""
Sets the configuration file
"""
self._strConfigurationFile = _strConfigurationFile
def getConfigurationFile(self):
"""
Returns the configuration file
"""
return self._strConfigurationFile
def setRequiredPluginConfiguration(self, _strPluginName=None):
if _strPluginName is None:
self._listRequiredConfigurationPluginNames.append(self._strPluginName)
else:
self._listRequiredConfigurationPluginNames.append(_strPluginName)
def createPlugin(self):
"""
Creates a plugin instance
"""
edPlugin = None
exceptionObject = None
try:
edFactoryPlugin = EDFactoryPlugin()
edPlugin = edFactoryPlugin.loadPlugin(self.getPluginName())
except ImportError, exceptionObject:
strWarningMessage = "Could not create the plugin: %s, reason: %s" % (self.getPluginName(), exceptionObject)
EDVerbose.WARNING(strWarningMessage)
if edPlugin is None:
if exceptionObject is None:
EDVerbose.error("EDTestCasePlugin.createPlugin: Could not create plugin: " + self.getPluginName())
return edPlugin
def preProcess(self, _edObject=None):
"""
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("*** EDPluginDCTWriteSinogramv1_0.preProcess")
pyStrPathToInputCIFFile = self.getDataInput().getIntegratedIntensities(
).getPath().getValue()
EDVerbose.DEBUG("This is the file which will be analyzed: %s" %
pyStrPathToInputCIFFile)
self.pystrPathToSinogramsDir = self.getDataInput(
).getSinogramDirectory().getPath().getValue()
if not PyOs.path.isdir(self.pystrPathToSinogramsDir):
PyOs.makedirs(self.pystrPathToSinogramsDir)
self.pystrSinogramPrefix = self.getDataInput(
).getSinogramFileNamePrefix().getValue()
EDVerbose.DEBUG(
"Now generation of the SinoGrams, Path: %s, Prefix= %s" %
(self.pystrPathToSinogramsDir, self.pystrSinogramPrefix))
if (not EDUtilsPath.existPath(pyStrPathToInputCIFFile)):
pyStrErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess", pyStrPathToInputFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
# File exists, try to read it with the CIF library
try:
self.m_cifPowderData = CIF()
self.m_cifPowderData.loadCIF(pyStrPathToInputCIFFile)
EDVerbose.DEBUG("Parsing of the CIF file %s successful" %
pyStrPathToInputCIFFile)
except Exception:
pyStrErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
"EDPluginDCTWriteSinogramv1_0.preProcess: Error when trying to read CIF file : %s"
% pyStrPathToInputCIFFile)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
# Just raise the exception in order to not loose the error stack trace
raise
if not self.m_cifPowderData.exists("_tomo_scan_type"):
EDVerbose.DEBUG(
"How do you want to generate a Sinogram if you are lacking essential things like the scan type !!!!"
)
raise
self.pydMetaDataEDF = self.m_cifPowderData.copy(
) #This is a simple python dictionary
if self.pydMetaDataEDF.has_key("loop_"):
self.pydMetaDataEDF.pop("loop_")
if self.pydMetaDataEDF.has_key("_synchrotron_photon-flux"):
self.pydMetaDataEDF.pop("_synchrotron_photon-flux")
if self.pydMetaDataEDF.has_key("_synchrotron_ring-intensity"):
self.pydMetaDataEDF.pop("_synchrotron_ring-intensity")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_rotation"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_rotation")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_x"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_x")
if self.pydMetaDataEDF.has_key("_tomo_spec_displ_z"):
self.pydMetaDataEDF.pop("_tomo_spec_displ_z")
self.powderIntegrator = PowderIntegrator(self.m_cifPowderData)
self.pyintXpos, self.pyintYpos = self.powderIntegrator.getSinogramPosition(
)
(Xmax, Ymax) = self.powderIntegrator.getSinogramSize()
self.pydProcessSinograms = {}
for pystrSinogramSuffix in [
"PhotonFlux", "IntegratedRaw", "IntegratedCor"
]:
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
self.pystrSinogramPrefix + "Sinogram" + pystrSinogramSuffix)
self.pydProcessSinograms[
pystrSinogramFullPath] = pystrSinogramSuffix
if self.m_cifPowderData.exists("_pd_sum_2theta_range_min"):
for basename in ["Raw", "Cor"]:
startregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_min"])
stopregion = float(
self.m_cifPowderData["_pd_sum_2theta_range_max"])
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix, int(
round(startregion)), int(round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir, pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
else:
for oneloop in self.m_cifPowderData["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
startregion = float(i["_pd_sum_2theta_range_min"])
stopregion = float(i["_pd_sum_2theta_range_max"])
for basename in ["Raw", "Cor"]:
pystrSinogramFilename = "%sSinogramROI%i-%i%s" % (
self.pystrSinogramPrefix,
int(round(startregion)), int(
round(stopregion)), basename)
pystrSinogramFullPath = PyOs.path.join(
self.pystrPathToSinogramsDir,
pystrSinogramFilename)
self.pydProcessSinograms[pystrSinogramFullPath] = [
startregion, stopregion
]
def configure(self):
"""
Configures the plugin from the configuration file with the following
parameters
- The shell that will execute the script
- Script executor
- Script executable to be invoked
- Path to CCP4 setup file if required
- The 3rd party executable installed version
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning(
"EDPluginExecProcessXIA2CORE.configure: No plugin item defined."
)
xsPluginItem = XSPluginItem()
if (self.getExecutable() is None):
strExecutable = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE)
if (strExecutable == None):
strErrorMessage = "Configuration parameter missing: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if (os.path.exists(strExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE + " : " + strExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setExecutable(strExecutable)
if (self.getConfigXIA2COREType() is None):
strXIA2COREType = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE)
if (strXIA2COREType == None):
strErrorMessage = "Configuration parameter not set: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE
EDVerbose.DEBUG(strErrorMessage)
else:
# FIXME test that this is a legal name
self.__strConfigXIA2COREType = strXIA2COREType
strVersion = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING)
if (strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure: No configuration parameter found for: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strLogFileName == None):
self.setLogFileName(self.getBaseName() + ".log")
if (self.__strErrorLogFileName == None):
self.setErrorLogFileName(self.getBaseName() + ".err")
if self.__strExecutable is None:
EDVerbose.ERROR("Executable not defined in configuration file")
# shall we raise an exception?
self.__strPathToHostNamePidFile = os.path.join(
self.getWorkingDirectory(),
os.path.basename(self.__strExecutable) + "_hostNamePid.txt")
return
