def readHeaderADSC(self, _strImageFileName):
"""
This method reads the header from an ADSC image and returns a dictionary.
Ideally this method should be a part of another (exec) plugin.
"""
pyFile = None
dictionary = None
try:
pyFile = open(_strImageFileName, "r")
except:
EDVerbose.warning("**** EDPluginExecReadImageHeaderADSCv10.readHeaderADSC: couldn't open file: " + _strImageFileName)
if (pyFile != None):
EDVerbose.DEBUG("EDPluginExecReadImageHeaderADSCv10.readHeaderADSC: Reading header from image " + _strImageFileName)
pyFile.seek(0, 0)
strLine = pyFile.readline()
if strLine[0] == "{":
dictionary = {}
strLine = pyFile.readline()
while strLine[0] != "}" :
listSplit = strLine.split("=")
strKeyword = listSplit[0]
listSplitValue = listSplit[1].split(";")
strValue = listSplitValue[0]
dictionary[strKeyword] = strValue
strLine = pyFile.readline()
pyFile.close()
return dictionary
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of
compatible versions
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.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.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.configure")
pluginConfiguration = self.getConfiguration()
if pluginConfiguration != None:
strSymopHome = EDConfiguration.getStringParamValue(
pluginConfiguration, self.strCONF_SYMOP_HOME)
if (strSymopHome == None):
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % (
'EDPluginControlKappaStrategyv2_0.configure',
self.strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
strSymopHome = EDConfiguration.getStringParamValue(
pluginConfiguration, "KAPPA")
if (strSymopHome == None or strSymopHome != "ON"):
#self.strPluginStrategyName = "EDPluginControlStrategyv10"
#self.strPluginStrategyName = "EDPluginControlStrategyv2_0"
self.KappaStrategy = 0
else:
self.KappaStrategy = 1
def getEdnaUserTempFolder(cls):
"""
Returns the name of a temporary folder that is unique for a given user.
"""
if cls._EDNA_USERTEMPFOLDER is None:
if os.environ.has_key("EDNA_USERTEMPFOLDER"):
cls._EDNA_USERTEMPFOLDER = os.environ["EDNA_USERTEMPFOLDER"]
if not os.path.exists(cls._EDNA_USERTEMPFOLDER):
EDVerbose.warning(
"EDNA_USERTEMPFOLDER environment variable is set to %s put the directory does not exist!"
% cls._EDNA_USERTEMPFOLDER)
cls._EDNA_USERTEMPFOLDER = None
elif (not os.access(cls._EDNA_USERTEMPFOLDER, os.W_OK)):
EDVerbose.warning(
"EDNA_USERTEMPFOLDER environment variable is set to %s put the directory cannot be accessed!"
% cls._EDNA_USERTEMPFOLDER)
cls._EDNA_USERTEMPFOLDER = None
if cls._EDNA_USERTEMPFOLDER is None:
strEdnaTempFileDir = tempfile.gettempdir()
try:
# Working on Windows and Linux:
strUserName = getpass.getuser()
except Exception:
# Working on MacOS:
strUserName = os.getlogin()
bIsOk = False
# Check that we have write access to this directory:
if os.access(strEdnaTempFileDir, os.W_OK) and os.access(
strEdnaTempFileDir, os.X_OK):
cls._EDNA_USERTEMPFOLDER = os.path.join(
strEdnaTempFileDir, "edna-%s" % strUserName)
# Check that we have write access to this directory:
if not os.path.exists(cls._EDNA_USERTEMPFOLDER):
try:
os.mkdir(cls._EDNA_USERTEMPFOLDER)
except Exception:
EDVerbose.WARNING(
"Error when trying to create the directory %s"
% cls._EDNA_USERTEMPFOLDER)
if os.access(cls._EDNA_USERTEMPFOLDER,
os.W_OK) and os.access(
cls._EDNA_USERTEMPFOLDER, os.X_OK):
bIsOk = True
if not bIsOk:
# We cannot use the edna-<user name> folder...
EDVerbose.WARNING(
"EDUtilsFile.getEdnaUserTempFolder: cannot access user temporary directory %s"
% cls._EDNA_USERTEMPFOLDER)
# Create temporary directory
cls._EDNA_USERTEMPFOLDER = tempfile.mkdtemp(prefix="edna-")
EDVerbose.WARNING(
"Created temporary directory for this session: %s" %
cls._EDNA_USERTEMPFOLDER)
EDVerbose.WARNING(
"If you would like to continue to use this directory for future sessions"
)
EDVerbose.WARNING(
"please set then environment variable EDNA_USERTEMPFOLDER to %s"
% cls._EDNA_USERTEMPFOLDER)
return cls._EDNA_USERTEMPFOLDER
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of
compatible versions
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.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.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
strRaddoseError = self.readProcessErrorLogFile()
if((strRaddoseError is not None) and (strRaddoseError != "")):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', 'EDPluginRaddosev10', strRaddoseError)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
resultDict = self.analyseScriptLogFileName(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()))
strSolvent = self.__dictResults[ EDPluginRaddosev10.__strSOLVENT ]
# ugly workaround while waiting for RADDOSE XML output file
strAbsorbedDose = None
for strAbsorbedDoseKeyword in EDPluginRaddosev10.__listABSORBED_DOSE:
strAbsorbedDose = self.__dictResults[ strAbsorbedDoseKeyword ]
if (strAbsorbedDose is not None):
break
if(strSolvent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', "Raddose", "No Result for Keyword [" + EDPluginRaddosev10.__strSOLVENT + "] see: " + self.getScriptLogFileName())
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if(strAbsorbedDose is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', "Raddose", "No Result for Keyword [" + strAbsorbedDoseKeyword + "] see: " + self.getScriptLogFileName())
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
self.__fSolvent = float(strSolvent)
if(self.__fSolvent < EDPluginRaddosev10.__iMIN_SOLVENT_PERCENTAGE or self.__fSolvent > EDPluginRaddosev10.__iMAX_SOLVENT_PERCENTAGE):
warningMessage = "Inconsistent solvent percentage value: %.1f" % self.__fSolvent
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
iNumberOfImages = self.getDataInput().getNumberOfImages().getValue()
fExposureTimePerImageInSec = self.getDataInput().getBeamExposureTime().getValue()
fTotalExposureTime = iNumberOfImages * fExposureTimePerImageInSec
fAbsorbedDoseSpeed = float(strAbsorbedDose) / fTotalExposureTime
xsDataAbsorbedDoseRate = XSDataAbsorbedDoseRate(fAbsorbedDoseSpeed)
xsDataAbsorbedDose = XSDataDouble(float(strAbsorbedDose))
self.__fTimeToReachHendersonLimit = EDPluginRaddosev10.__fHENDERSON_LIMIT / fAbsorbedDoseSpeed
xsDataRaddosev10Output = XSDataRaddoseOutput()
xsDataRaddosev10Output.setAbsorbedDose(xsDataAbsorbedDose)
xsDataRaddosev10Output.setAbsorbedDoseRate(xsDataAbsorbedDoseRate)
xsDataRaddosev10Output.setTimeToReachHendersonLimit(XSDataTime(self.__fTimeToReachHendersonLimit))
xsDataFilePathToLog = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))
xsDataRaddosev10Output.setPathToLogFile(xsDataFilePathToLog)
self.setDataOutput(xsDataRaddosev10Output)
def setEdnaTestDataPath(cls, value):
"""
This class method initializes the path to the test data (probably unused)
"""
cls._EDNA_TESTDATA = os.path.abspath(value)
if not os.path.isdir(cls._EDNA_TESTDATA):
EDVerbose.warning("EDNA_TESTDATA environment variable is set to %s put the directory does not exist!" % cls._EDNA_TESTDATA)
cls._EDNA_TESTDATA = None
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.configure")
strSymopHome = self.config.get(self._strCONF_SYMOP_HOME)
if strSymopHome is None:
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlStrategyv1_2.configure', self._strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.setSymopHome(strSymopHome)
def setEdnaTestDataPath(cls, value):
"""
This class method initializes the path to the test data (probably unused)
"""
cls._EDNA_TESTDATA = os.path.abspath(value)
if not os.path.isdir(cls._EDNA_TESTDATA):
EDVerbose.warning(
"EDNA_TESTDATA environment variable is set to %s put the directory does not exist!"
% cls._EDNA_TESTDATA)
cls._EDNA_TESTDATA = None
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.configure")
strSymopHome = self.config.get(self._strCONF_SYMOP_HOME)
if strSymopHome is None:
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlStrategyv1_2.configure', self._strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.setSymopHome(strSymopHome)
def setConfiguration(_edConfiguration):
"""
"""
EDVerbose.DEBUG("EDApplication.setConfiguration")
EDApplication.synchronizeOn()
if (_edConfiguration == None):
EDVerbose.warning("EDApplication.setConfiguration: Configuration is None!")
else:
EDApplication.__edConfiguration = _edConfiguration
EDApplication.synchronizeOff()
def doFailureActionRaddose(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.doFailureActionRaddose")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlStrategyv1_2.doFailureActionRaddose")
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv1_2.doFailureActionRaddose', self._strPluginRaddoseName, "Raddose failure")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeBest(self)
def doFailureActionAlignment(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG("EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment")
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment', self.strPluginAlignmentName, "STACAlignment failure")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeSimpleStrategy(_edPlugin)
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)
# Load the configuration file
if(self.__strConfigurationFileName is None):
self.__strConfigurationHome = EDApplication.getConfigurationHome(self.__strPluginName)
self.__strConfigurationFileName = os.path.abspath(os.path.join(self.__strConfigurationHome, "XSConfiguration_%s.xml" % EDUtilsPath.getEdnaSite()))
if (os.path.exists(self.__strConfigurationFileName)):
EDVerbose.screen("Loading Configuration file: %s" % self.__strConfigurationFileName)
edConfiguration = EDConfiguration(self.__strConfigurationFileName)
self.setConfiguration(edConfiguration)
self.loadConfiguration()
EDVerbose.DEBUG("EDApplication.preProcess: Checking... Number of plugins...: %d" % EDApplication.__edConfiguration.getPluginListSize())
pyDictionary = {}
pyDictionary[ "${EDNA_HOME}" ] = EDUtilsPath.getEdnaHome()
if self.getDataInputFilePath() is not None:
self.__strXMLData = EDUtilsFile.readFileAndParseVariables(self.getDataInputFilePath(), pyDictionary)
else:
EDVerbose.warning("Cannot find configuration file: %s" % self.__strConfigurationFileName)
# Create the application working directory
if(self.__strWorkingDir is None):
self.__strWorkingDir = self.__strApplicationInstanceName
self.createApplicationWorkingDirectory()
def doFailureActionRaddose(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG("EDPluginControlStrategyv10.doFailureActionRaddose")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlStrategyv10.doFailureActionRaddose")
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.doFailureActionRaddose', self.__strPluginRaddoseName, "Raddose failure")
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
self.executeBest(self)
def getEdnaUserTempFolder(cls):
"""
Returns the name of a temporary folder that is unique for a given user.
"""
if cls._EDNA_USERTEMPFOLDER is None:
if os.environ.has_key("EDNA_USERTEMPFOLDER"):
cls._EDNA_USERTEMPFOLDER = os.environ["EDNA_USERTEMPFOLDER"]
if not os.path.exists(cls._EDNA_USERTEMPFOLDER):
EDVerbose.warning(
"EDNA_USERTEMPFOLDER environment variable is set to %s put the directory does not exist!"
% cls._EDNA_USERTEMPFOLDER
)
cls._EDNA_USERTEMPFOLDER = None
elif not os.access(cls._EDNA_USERTEMPFOLDER, os.W_OK):
EDVerbose.warning(
"EDNA_USERTEMPFOLDER environment variable is set to %s put the directory cannot be accessed!"
% cls._EDNA_USERTEMPFOLDER
)
cls._EDNA_USERTEMPFOLDER = None
if cls._EDNA_USERTEMPFOLDER is None:
strEdnaTempFileDir = tempfile.gettempdir()
try:
# Working on Windows and Linux:
strUserName = getpass.getuser()
except Exception:
# Working on MacOS:
strUserName = os.getlogin()
bIsOk = False
# Check that we have write access to this directory:
if os.access(strEdnaTempFileDir, os.W_OK) and os.access(strEdnaTempFileDir, os.X_OK):
cls._EDNA_USERTEMPFOLDER = os.path.join(strEdnaTempFileDir, "edna-%s" % strUserName)
# Check that we have write access to this directory:
if not os.path.exists(cls._EDNA_USERTEMPFOLDER):
try:
os.mkdir(cls._EDNA_USERTEMPFOLDER)
except Exception:
EDVerbose.WARNING("Error when trying to create the directory %s" % cls._EDNA_USERTEMPFOLDER)
if os.access(cls._EDNA_USERTEMPFOLDER, os.W_OK) and os.access(cls._EDNA_USERTEMPFOLDER, os.X_OK):
bIsOk = True
if not bIsOk:
# We cannot use the edna-<user name> folder...
EDVerbose.WARNING(
"EDUtilsFile.getEdnaUserTempFolder: cannot access user temporary directory %s"
% cls._EDNA_USERTEMPFOLDER
)
# Create temporary directory
cls._EDNA_USERTEMPFOLDER = tempfile.mkdtemp(prefix="edna-")
EDVerbose.WARNING("Created temporary directory for this session: %s" % cls._EDNA_USERTEMPFOLDER)
EDVerbose.WARNING("If you would like to continue to use this directory for future sessions")
EDVerbose.WARNING(
"please set then environment variable EDNA_USERTEMPFOLDER to %s" % cls._EDNA_USERTEMPFOLDER
)
return cls._EDNA_USERTEMPFOLDER
def getPluginConfiguration(self, _strConfigurationFileName):
"""
Returns the plugin configuration from a configuration file
"""
xsPluginItem = None
edConfiguration = EDConfiguration(_strConfigurationFileName)
if(edConfiguration != None):
xsPluginItem = edConfiguration.getXSConfigurationItem(self.getPluginName())
if(xsPluginItem == None):
EDVerbose.warning("EDTestCasePluginUnit.getPluginConfiguration: Could not get configuration plugin item for: " + self.getPluginName())
else:
EDVerbose.warning("EDTestCasePluginUnit.getPluginConfiguration: Could not load Configuration: " + _strConfigurationFileName)
return xsPluginItem
def getEdnaSite(cls):
"""
Returns the EDNA_SITE variable from environment
"""
# EDNA Site
if(cls._EDNA_SITE == None):
cls._EDNA_SITE = os.environ.get("EDNA_SITE")
if(cls._EDNA_SITE is None):
EDVerbose.warning("EDUtilsPath.getEdnaSite: EDNA_SITE not set, using EDNA_SITE='default'")
cls._EDNA_SITE = "default"
else:
EDVerbose.DEBUG("EDUtilsPath.getEdnaSite: EDNA_SITE is set: %s" % cls._EDNA_SITE)
return cls._EDNA_SITE
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 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 preProcess(self, _edObject=None):
"""
Preprocess of the plugin:
check parameters and extract from EDNA format into something more simple & pythonic
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginPyarchThumbnailv10.preProcess")
sdi = self.getDataInput()
if sdi.getInputImagePath() is not None:
self.inputFilename = sdi.getInputImagePath().getPath().getValue()
if not os.path.isfile(self.inputFilename):
EDVerbose.ERROR(
"The input file provided is not a valid file: " +
self.inputFilename)
raise "Not a valid file " + self.inputFilename
# Output path
strImageNameWithoutExt = os.path.basename(
os.path.splitext(self.inputFilename)[0])
strImageDirname = os.path.dirname(self.inputFilename)
strOutputDirname = self.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.strOutputPath = os.path.join(strOutputDirname,
strImageNameWithoutExt + ".jpeg")
self.strOutputPathThumb = os.path.join(
strOutputDirname, strImageNameWithoutExt + ".thumb.jpeg")
def newFile(self, filename="test", size=(0, 0), metadata={}):
"""this is a method to create a new empty file
@param filename: name of the file to create, the size and the extension will be added.
@type filename: string
@type size: 2-tuple of integers
@param size: the size of the image to create
"""
if len(size) != 2:
EDVerbose.error("Error in the size of the size-tuple")
raise Exception("Error in the size of the size-tuple")
if size[0] < 0:
EDVerbose.error("Error in the X part of the size tuple")
raise Exception("Error in the X part of the size tuple")
if size[1] < 0:
EDVerbose.error("Error in the Y part of the size tuple")
raise Exception("Error in the Y part of the size tuple")
emptyNParray = numpy.zeros(size, dtype="float32")
self.data[filename] = emptyNParray
self.headers[filename] = metadata
self.size[filename] = size
fullFilename = "%sSize%ix%i.edf" % ((filename, ) + size)
if os.path.isfile(fullFilename):
EDVerbose.warning("Warning, I am going to overwrite the file %s " %
fullFilename)
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.data[filename] = self.edf[filename].GetData(0)
self.headers[filename] = self.edf[filename].GetHeader(0)
except Exception:
EDVerbose.error("[ERROR] in reading file %s" % filename)
self.synchronizeOff()
if self.data[filename].shape != size:
self.data[filename] = emptyNParray
self.headers[filename] = metadata
else:
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.edf[filename].WriteImage(self.headers[filename],
self.data[filename],
Append=0)
except Exception:
EDVerbose.error("[ERROR] in opening and creating file %s" %
filename)
self.synchronizeOff()
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- Excpected image size
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginControlDiffractionCTv1_2.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strImageSize = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE)
if(strImageSize == None):
EDVerbose.WARNING("EDPluginControlDiffractionCTv1_2.configure: No configuration parameter found for: %s, using default value: %s " % (\
EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE, self.iImageSize))
else:
self.iImageSize = int(strImageSize)
def configure(self):
EDPluginExecProcessScript.configure(self)
EDVerbose.DEBUG("EDPluginLabelitv1_1.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginLabelitv1_1.configure: No Labelit plugin item defined.")
xsPluginItem = XSPluginItem()
strPathToLabelitSetpathScript = EDConfiguration.getStringParamValue(xsPluginItem, \
EDPluginLabelitv1_1.CONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
if(strPathToLabelitSetpathScript == None):
strErrorMessage = "EDPluginLabelitv1_1.configure : Configuration parameter missing: " + \
EDPluginLabelitv1_1.CONF_PATH_TO_LABELIT_SETPATH_SCRIPT
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.setPathToLabelitSetpathScript(strPathToLabelitSetpathScript)
def getEdnaSite(cls):
"""
Returns the EDNA_SITE variable from environment
"""
# EDNA Site
if (cls._EDNA_SITE == None):
cls._EDNA_SITE = os.environ.get("EDNA_SITE")
if (cls._EDNA_SITE is None):
EDVerbose.warning(
"EDUtilsPath.getEdnaSite: EDNA_SITE not set, using EDNA_SITE='default'"
)
cls._EDNA_SITE = "default"
else:
EDVerbose.DEBUG(
"EDUtilsPath.getEdnaSite: EDNA_SITE is set: %s" %
cls._EDNA_SITE)
return cls._EDNA_SITE
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.configure")
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
strWarningMessage = EDMessage.WARNING_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % ('EDPluginControlStrategyv1_2.configure', self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHome = self.getStringConfigurationParameterValue(self._strCONF_SYMOP_HOME)
if(strSymopHome == None):
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlStrategyv1_2.configure', self._strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.setSymopHome(strSymopHome)
def getPluginConfiguration(self, _strConfigurationFileName):
"""
Returns the plugin configuration from a configuration file
"""
xsPluginItem = None
edConfiguration = EDConfiguration(_strConfigurationFileName)
if (edConfiguration != None):
xsPluginItem = edConfiguration.getXSConfigurationItem(
self.getPluginName())
if (xsPluginItem == None):
EDVerbose.warning(
"EDTestCasePluginUnit.getPluginConfiguration: Could not get configuration plugin item for: "
+ self.getPluginName())
else:
EDVerbose.warning(
"EDTestCasePluginUnit.getPluginConfiguration: Could not load Configuration: "
+ _strConfigurationFileName)
return xsPluginItem
def getDataInput(self, _strDataInputKey=None):
"""
Returns the Plugin Input Data for a particular key.
If the key is not provided a default key is used.
"""
oValue = None
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.getDefaultInputDataKey()
if (strDataInputKey in self.__dictXMLDataInput.keys()):
oValue = self.__dictXMLDataInput[ strDataInputKey ]
else:
strErrorMessage = self.getPluginName() + ".getDataInput, no input data defined for key: " + strDataInputKey
EDVerbose.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
if isinstance(oValue, (str, unicode)):
oValue = self.xsDataXmlToObject(oValue)
return oValue
def doFailureActionAlignment(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
EDVerbose.DEBUG(
"EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment"
)
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment"
)
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaReorientationStrategyv2_0.doFailureActionAlignment',
self.strPluginAlignmentName, "STACAlignment failure")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeSimpleStrategy(_edPlugin)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.configure")
strSymopHome = self.config.get(self.strCONF_SYMOP_HOME)
if strSymopHome is None:
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlKappaStrategyv2_0.configure', self.strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
bKappaOn = self.config.get("KAPPA")
if bKappaOn:
#self.strPluginStrategyName = "EDPluginControlStrategyv10"
#self.strPluginStrategyName = "EDPluginControlStrategyv2_0"
self.KappaStrategy = 1
else:
self.KappaStrategy = 0
def configure(self):
"""
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv10.configure")
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
warningMessage = EDMessage.WARNING_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % ('EDPluginControlStrategyv10.configure', self.getPluginName())
EDVerbose.DEBUG(warningMessage)
else:
strSymopHome = EDConfiguration.getStringParamValue(pluginConfiguration, self.__strCONF_SYMOP_HOME)
if(strSymopHome == None):
warningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlStrategyv10.configure', self.__strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.configure")
strSymopHome = self.config.get(self.strCONF_SYMOP_HOME)
if strSymopHome is None:
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlKappaStrategyv2_0.configure', self.strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
bKappaOn = self.config.get("KAPPA")
if bKappaOn:
#self.strPluginStrategyName = "EDPluginControlStrategyv10"
#self.strPluginStrategyName = "EDPluginControlStrategyv2_0"
self.KappaStrategy = 1
else:
self.KappaStrategy = 0
def newFile(self, filename="test", size=(0, 0), metadata={}):
"""this is a method to create a new empty file
@param filename: name of the file to create, the size and the extension will be added.
@type filename: string
@type size: 2-tuple of integers
@param size: the size of the image to create
"""
if len(size) != 2 :
EDVerbose.error("Error in the size of the size-tuple")
raise Exception("Error in the size of the size-tuple")
if size[0] < 0 :
EDVerbose.error("Error in the X part of the size tuple")
raise Exception("Error in the X part of the size tuple")
if size[1] < 0 :
EDVerbose.error("Error in the Y part of the size tuple")
raise Exception("Error in the Y part of the size tuple")
emptyNParray = numpy.zeros(size, dtype="float32")
self.data[ filename ] = emptyNParray
self.headers [ filename ] = metadata
self.size [ filename ] = size
fullFilename = "%sSize%ix%i.edf" % ((filename,) + size)
if os.path.isfile(fullFilename):
EDVerbose.warning("Warning, I am going to overwrite the file %s " % fullFilename)
self.synchronizeOn()
try:
self.edf [ filename ] = EdfFile(fullFilename)
self.data[ filename ] = self.edf[ filename ].GetData(0)
self.headers [ filename ] = self.edf[ filename ].GetHeader(0)
except Exception:
EDVerbose.error("[ERROR] in reading file %s" % filename)
self.synchronizeOff()
if self.data[ filename ].shape != size :
self.data[ filename ] = emptyNParray
self.headers [ filename ] = metadata
else:
self.synchronizeOn()
try:
self.edf[ filename ] = EdfFile(fullFilename)
self.edf[ filename ].WriteImage(self.headers [ filename ] , self.data [ filename ] , Append=0)
except Exception:
EDVerbose.error("[ERROR] in opening and creating file %s" % filename)
self.synchronizeOff()
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration == None):
strWarningMessage = EDMessage.WARNING_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % (
'EDPluginControlStrategyv1_2.configure', self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHome = self.getStringConfigurationParameterValue(
self._strCONF_SYMOP_HOME)
if (strSymopHome == None):
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % (
'EDPluginControlStrategyv1_2.configure',
self._strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.setSymopHome(strSymopHome)
def getEdnaPluginCachePath(cls):
"""This private method initializes the path to the plugin cache file"""
if cls._EDNA_PLUGINCACHE is None:
if "EDNA_PLUGINCACHE" in os.environ.keys():
cls._EDNA_PLUGINCACHE = os.environ["EDNA_PLUGINCACHE"]
strDirName = os.path.dirname(cls._EDNA_PLUGINCACHE)
if os.path.exists(cls._EDNA_PLUGINCACHE) and (not os.access(
cls._EDNA_PLUGINCACHE, os.W_OK)):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s but the file is not writeable!"
% cls._EDNA_PLUGINCACHE)
cls._EDNA_PLUGINCACHE = None
elif not os.path.exists(strDirName):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s put the parent directory does not exist!"
% cls._EDNA_PLUGINCACHE)
cls._EDNA_PLUGINCACHE = None
elif not os.access(strDirName, os.W_OK):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s put the parent directory cannot be accessed!"
% cls._EDNA_PLUGINCACHE)
cls._EDNA_PLUGINCACHE = None
if cls._EDNA_PLUGINCACHE is None:
strTempFileDir = EDUtilsPath.getEdnaUserTempFolder()
# We create a hash of the path in order to be able to reference several different EDNA_HOME
# caches in the same directory
strCacheFileName = hashlib.sha1(
os.getenv('EDNA_HOME')).hexdigest() + ".xml"
cls._EDNA_PLUGINCACHE = os.path.abspath(
os.path.join(strTempFileDir, strCacheFileName))
EDVerbose.DEBUG("EDFactoryPlugin: Path to plugin cache: %s" %
cls._EDNA_PLUGINCACHE)
return cls._EDNA_PLUGINCACHE
def getEdnaPluginCachePath(cls):
"""This private method initializes the path to the plugin cache file"""
if cls._EDNA_PLUGINCACHE is None:
if "EDNA_PLUGINCACHE" in os.environ.keys():
cls._EDNA_PLUGINCACHE = os.environ["EDNA_PLUGINCACHE"]
strDirName = os.path.dirname(cls._EDNA_PLUGINCACHE)
if os.path.exists(cls._EDNA_PLUGINCACHE) and (not os.access(cls._EDNA_PLUGINCACHE, os.W_OK)):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s but the file is not writeable!"
% cls._EDNA_PLUGINCACHE
)
cls._EDNA_PLUGINCACHE = None
elif not os.path.exists(strDirName):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s put the parent directory does not exist!"
% cls._EDNA_PLUGINCACHE
)
cls._EDNA_PLUGINCACHE = None
elif not os.access(strDirName, os.W_OK):
EDVerbose.warning(
"EDNA_PLUGINCACHE environment variable is set to %s put the parent directory cannot be accessed!"
% cls._EDNA_PLUGINCACHE
)
cls._EDNA_PLUGINCACHE = None
if cls._EDNA_PLUGINCACHE is None:
strTempFileDir = EDUtilsPath.getEdnaUserTempFolder()
# We create a hash of the path in order to be able to reference several different EDNA_HOME
# caches in the same directory
strCacheFileName = hashlib.sha1(os.getenv("EDNA_HOME")).hexdigest() + ".xml"
cls._EDNA_PLUGINCACHE = os.path.abspath(os.path.join(strTempFileDir, strCacheFileName))
EDVerbose.DEBUG("EDFactoryPlugin: Path to plugin cache: %s" % cls._EDNA_PLUGINCACHE)
return cls._EDNA_PLUGINCACHE
def configure(self):
"""
Configures the plugin with executable from configuration file
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcess.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginExecProcess.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strExecutable = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcess.CONF_EXEC_PROCESS_EXECUTABLE)
if(strExecutable == None):
EDVerbose.DEBUG("EDPluginExecProcess.configure: No configuration parameter found for: %s , using default value: %s"\
% (EDPluginExecProcess.CONF_EXEC_PROCESS_EXECUTABLE, self.getExecutable()))
else:
self.setExecutable(strExecutable)
# The execProcessTimeOut is deprecated, see bug #563
strTimeOut = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcess.CONF_EXEC_PROCESS_TIME_OUT)
if strTimeOut is not None:
EDVerbose.WARNING("Use of %s in plugin configuration is deprecated" % EDPluginExecProcess.CONF_EXEC_PROCESS_TIME_OUT)
EDVerbose.WARNING("Please use %s instead." % EDPlugin.CONF_TIME_OUT)
self.setTimeOut(strTimeOut)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.configure")
pluginConfiguration = self.getConfiguration()
if pluginConfiguration != None:
strSymopHome = EDConfiguration.getStringParamValue(pluginConfiguration, self.strCONF_SYMOP_HOME)
if(strSymopHome == None):
strWarningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % ('EDPluginControlKappaStrategyv2_0.configure', self.strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
strSymopHome = EDConfiguration.getStringParamValue(pluginConfiguration, "KAPPA")
if(strSymopHome == None or strSymopHome != "ON"):
#self.strPluginStrategyName = "EDPluginControlStrategyv10"
#self.strPluginStrategyName = "EDPluginControlStrategyv2_0"
self.KappaStrategy = 0
else:
self.KappaStrategy = 1
def getImageFileNameFromTemplate(self, _strTemplate, _iImageNumber):
bHashFound = False
bFinished = False
iFirstHash = None
iNoHashes = 0
strImageFileName = None
try:
for iIndex, pyChar in enumerate(_strTemplate):
if ((not bHashFound) and (not bFinished)):
if (pyChar == "#"):
iFirstHash = iIndex
bHashFound = True
else:
if ((pyChar != "#") and (not bFinished)):
bFinished = True
if (bHashFound and (not bFinished)):
iNoHashes += 1
strImageFileName = _strTemplate[ 0:iFirstHash ] + str(_iImageNumber).rjust(iNoHashes, "0")
except:
EDVerbose.warning("EDPluginMOSFLMGeneratePredictionv10: Couldn't transform template %s to file name" % _strTemplate)
strImageFileName = None
return strImageFileName
def configure(self):
"""
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlStrategyv10.configure")
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration == None):
warningMessage = EDMessage.WARNING_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % (
'EDPluginControlStrategyv10.configure', self.getPluginName())
EDVerbose.DEBUG(warningMessage)
else:
strSymopHome = EDConfiguration.getStringParamValue(
pluginConfiguration, self.__strCONF_SYMOP_HOME)
if (strSymopHome == None):
warningMessage = EDMessage.WARNING_NO_PARAM_CONFIGURATION_ITEM_FOUND_03 % (
'EDPluginControlStrategyv10.configure',
self.__strCONF_SYMOP_HOME, self.getPluginName())
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
strSymopHomeNorm = os.path.normpath(strSymopHome)
self.setSymopHome(strSymopHomeNorm)
def preProcess(self, _edObject=None):
"""
Preprocess of the plugin:
check parameters and extract from EDNA format into something more simple & pythonic
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginPyarchThumbnailv10.preProcess")
sdi = self.getDataInput()
if sdi.getInputImagePath() is not None:
self.inputFilename = sdi.getInputImagePath().getPath().getValue()
if not os.path.isfile(self.inputFilename):
EDVerbose.ERROR("The input file provided is not a valid file: " + self.inputFilename)
raise "Not a valid file " + self.inputFilename
# Output path
strImageNameWithoutExt = os.path.basename(os.path.splitext(self.inputFilename)[0])
strImageDirname = os.path.dirname(self.inputFilename)
strOutputDirname = self.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.strOutputPath = os.path.join(strOutputDirname, strImageNameWithoutExt + ".jpeg")
self.strOutputPathThumb = os.path.join(strOutputDirname, strImageNameWithoutExt + ".thumb.jpeg")
def setEdnaTestDataImagesPath(cls, value):
"""
This class method initializes the path to the test images downloaded from internet
"""
cls._EDNA_TESTIMAGES = os.path.abspath(value)
if os.path.exists(cls._EDNA_TESTIMAGES) and (not os.access(cls._EDNA_TESTIMAGES, os.W_OK)):
EDVerbose.warning("EDNA_TESTIMAGES environment variable is set to %s but the file is not writeable!" % cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
elif not os.path.exists(cls._EDNA_TESTIMAGES):
EDVerbose.warning("EDNA_TESTIMAGES environment variable is set to %s put the directory does not exist!" % cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
elif not os.access(cls._EDNA_TESTIMAGES, os.W_OK):
EDVerbose.warning("EDNA_TESTIMAGES environment variable is set to %s put the directory cannot be accessed!" % cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
def setEdnaTestDataImagesPath(cls, value):
"""
This class method initializes the path to the test images downloaded from internet
"""
cls._EDNA_TESTIMAGES = os.path.abspath(value)
if os.path.exists(cls._EDNA_TESTIMAGES) and (not os.access(
cls._EDNA_TESTIMAGES, os.W_OK)):
EDVerbose.warning(
"EDNA_TESTIMAGES environment variable is set to %s but the file is not writeable!"
% cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
elif not os.path.exists(cls._EDNA_TESTIMAGES):
EDVerbose.warning(
"EDNA_TESTIMAGES environment variable is set to %s put the directory does not exist!"
% cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
elif not os.access(cls._EDNA_TESTIMAGES, os.W_OK):
EDVerbose.warning(
"EDNA_TESTIMAGES environment variable is set to %s put the directory cannot be accessed!"
% cls._EDNA_TESTIMAGES)
cls._EDNA_TESTIMAGES = None
def createDNAFileDirectory(self, _strDNAFileDirectoryPath):
"""
Create a "DNA-files" directory - if possible.
"""
bSuccess = False
if (_strDNAFileDirectoryPath is not None):
if (os.path.exists(_strDNAFileDirectoryPath)):
EDVerbose.warning("Removing existing DNA files directory: %s" % _strDNAFileDirectoryPath)
if (os.access(_strDNAFileDirectoryPath, os.W_OK)):
shutil.rmtree(_strDNAFileDirectoryPath)
else:
EDVerbose.warning("Cannot remove existing DNA files directory!")
if (_strDNAFileDirectoryPath is not None):
# Check if directory one level up is writeable
strDNAFileBaseDirectory = os.path.split(_strDNAFileDirectoryPath)[0]
if (os.access(strDNAFileBaseDirectory, os.W_OK)):
EDVerbose.DEBUG("Creating DNA files directory: %s" % _strDNAFileDirectoryPath)
os.mkdir(_strDNAFileDirectoryPath)
bSuccess = True
else:
EDVerbose.warning("Cannot create DNA files directory: %s" % _strDNAFileDirectoryPath)
return bSuccess
def createDNAFileDirectory(self, _strDNAFileDirectoryPath):
"""
Create a "DNA-files" directory - if possible.
"""
bSuccess = False
if (_strDNAFileDirectoryPath is not None):
if (os.path.exists(_strDNAFileDirectoryPath)):
EDVerbose.warning("Removing existing DNA files directory: %s" % _strDNAFileDirectoryPath)
if (os.access(_strDNAFileDirectoryPath, os.W_OK)):
shutil.rmtree(_strDNAFileDirectoryPath)
else:
EDVerbose.warning("Cannot remove existing DNA files directory!")
if (_strDNAFileDirectoryPath is not None):
# Check if directory one level up is writeable
strDNAFileBaseDirectory = os.path.split(_strDNAFileDirectoryPath)[0]
if (os.access(strDNAFileBaseDirectory, os.W_OK)):
EDVerbose.DEBUG("Creating DNA files directory: %s" % _strDNAFileDirectoryPath)
os.mkdir(_strDNAFileDirectoryPath)
bSuccess = True
else:
EDVerbose.warning("Cannot create DNA files directory: %s" % _strDNAFileDirectoryPath)
return bSuccess
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
def process(self, _edObject=None):
"""
This is the main method of the plugin, it does the job, not the EDNA name conversions which were done in the preprocess.
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecThumbnailv10.process")
# try:
# except Exception:
# edfImage = EDF(self.inputFilename)
# self.npaImage = edfImage.GetData(0)
# Read the image using FABIO
isRGB = False
pilOutputImage = None
if self.inputFilename is not None:
try:
fabioImage = openimage(self.inputFilename)
self.npaImage = fabioImage.data
except Exception:
pilInputImage = Image.open(self.inputFilename)
x, y = pilInputImage.size
ImageFile.MAXBLOCK = x * y
if pilInputImage.mode == "1":
self.npaImage = numpy.asarray(pilInputImage).astype(
"uint8")
isRGB = False
elif pilInputImage.mode == "F":
self.npaImage = numpy.asarray(pilInputImage)
isRGB = False
elif pilInputImage.mode == "L":
self.npaImage = numpy.asarray(pilInputImage)
isRGB = False
elif pilInputImage.mode == "P":
self.npaImage = numpy.asarray(pilInputImage.convert("RGB"))
isRGB = True
elif pilInputImage.mode == "RGB":
self.npaImage = numpy.asarray(pilInputImage)
isRGB = True
elif pilInputImage.mode == "CMJK":
self.npaImage = numpy.asarray(pilInputImage.convert("RGB"))
isRGB = True
dtype = self.npaImage.dtype
NPAImageFloat = None
# crop border
if len(self.cropBorders) > 0:
if len(self.cropBorders) == 1:
crop0 = self.cropBorders[0]
crop1 = self.cropBorders[0]
else:
crop0 = self.cropBorders[0]
crop1 = self.cropBorders[1]
if isRGB:
self.npaImage = self.npaImage[crop0:-crop0, crop1:crop1, :]
else:
self.npaImage = self.npaImage[crop0:-crop0, crop1:crop1]
# Set maxima and minima
if (self.minLevelUnit is not None) or (self.maxLevelUnit is not None):
sortedArray = self.npaImage.flatten()
sortedArray.sort()
if self.minLevel is not None:
self.normalize = True
if isRGB:
EDVerbose.warning(
"It is not allowed to set Min with RGB data")
else:
if self.minLevelUnit in ["%", "percent"]:
self.minLevel = sortedArray[int(
round(float(self.minLevel) * sortedArray.size /
100.0))]
if isinstance(self.npaImage[0, 0], int):
self.npaImage = numpy.maximum(
self.npaImage,
int(self.minLevel) * numpy.ones_like(self.npaImage))
else:
self.npaImage = numpy.maximum(
self.npaImage,
self.minLevel * numpy.ones_like(self.npaImage))
if self.maxLevel is not None:
self.normalize = True
if isRGB:
EDVerbose.warning(
"It is not allowed to set Max with RGB data")
else:
if self.maxLevelUnit in ["%", "percent"]:
self.maxLevel = sortedArray[int(
round(float(self.maxLevel) * sortedArray.size /
100.0))]
if isinstance(self.npaImage[0, 0], int):
self.npaImage = numpy.minimum(
self.npaImage,
int(self.maxLevel) * numpy.ones_like(self.npaImage))
else:
self.npaImage = numpy.minimum(
self.npaImage,
self.maxLevel * numpy.ones_like(self.npaImage))
# Scipy filters come here:
if len(self.gaussianBlur) > 0:
if len(self.gaussianBlur) == 1:
kernel = (self.gaussianBlur[0], self.gaussianBlur[0])
else:
kernel = (self.gaussianBlur[0], self.gaussianBlur[1])
if isRGB:
kernel = (kernel[0], kernel[1], 0)
self.npaImage = scipy.ndimage.gaussian_filter(
self.npaImage, kernel)
if len(self.dilatation) > 0:
if len(self.dilatation) == 1:
kernel = (self.dilatation[0], self.dilatation[0])
else:
kernel = (self.dilatation[0], self.dilatation[1])
if isRGB:
kernel = (kernel[0], kernel[1], 0)
self.npaImage = scipy.ndimage.morphology.grey_dilation(
self.npaImage, kernel)
#Normalization ; equalization
if (self.normalize is True) or (self.equalize is True):
if isRGB is True:
self.npaImage = numpy.asarray(
ImageOps.equalize(Image.fromarray(self.npaImage)))
else:
EDVerbose.DEBUG("EDPluginExecThumbnailv10: Normalization")
vmin = self.npaImage.min()
vmax = self.npaImage.max()
NPAImageFloat = (self.npaImage.astype(numpy.float32) -
float(vmin)) / (float(vmax) - float(vmin))
if (self.equalize == True):
nbr_bins = 64
NPAImageFloatFlat = NPAImageFloat.flatten()
imhist, bins = numpy.histogram(
NPAImageFloatFlat, nbr_bins,
normed=True) #get image histogram
cdf = imhist.cumsum() #cumulative distribution function
ncdf = cdf / cdf[
-1] #normalized cumulative distribution function
# print ncdf
NPAImageFloat2Flat = numpy.interp(NPAImageFloatFlat, bins,
[0] + ncdf.tolist())
NPAImageFloat = NPAImageFloat2Flat.reshape(
NPAImageFloat.shape)
EDVerbose.DEBUG("Equalize: min= %f, max= %f" %
(NPAImageFloat.min(), NPAImageFloat.max()))
#Gamma and logarithm scale
if ((self.log is True) or (self.gamma != 1)) and (
NPAImageFloat is None): # then we need the array in float
if dtype == numpy.uint8:
NPAImageFloat = self.npaImage.astype(numpy.float32) / 255.0
elif dtype == numpy.uint16:
NPAImageFloat = self.npaImage.astype(numpy.float32) / 65535.0
else:
NPAImageFloat = self.npaImage.astype(numpy.float32)
if self.log is True:
NPAImageFloat = numpy.log(1 - NPAImageFloat.min() + NPAImageFloat)
vmin = NPAImageFloat.min()
vmax = NPAImageFloat.max()
NPAImageFloat = (NPAImageFloat - vmin) / (vmax - vmin)
if self.gamma != 1:
if dtype not in [numpy.uint8, numpy.uint16]:
vmin = NPAImageFloat.min()
vmax = NPAImageFloat.max()
NPAImageFloat = (NPAImageFloat - vmin) / (vmax - vmin)
NPAImageInt = (255.0 * (NPAImageFloat**self.gamma)).astype("uint8")
else: #if (self.gamma == 1):
if NPAImageFloat is None:
if dtype == numpy.uint8:
NPAImageInt = self.npaImage
elif dtype == numpy.uint16:
NPAImageInt = (self.npaImage / 256).astype(numpy.uint8)
else: #for float or a signed integer
vmin = self.npaImage.min()
vmax = self.npaImage.max()
NPAImageInt = (
(self.npaImage.astype(numpy.float32) - vmin) /
(vmax - vmin) * 255.0).astype(numpy.uint8)
else:
vmin = NPAImageFloat.min()
vmax = NPAImageFloat.max()
EDVerbose.DEBUG(
"EDPluginExecThumbnailv10: NPAImageFloat => NPAImageInt min=%s max =%s"
% (vmin, vmax))
NPAImageInt = ((NPAImageFloat - vmin) * 255.0 /
(vmax - vmin)).astype(numpy.uint8)
#COnversion back to PIL mode
if isRGB is True:
pilOutputImage = Image.fromarray(NPAImageInt, 'RGB')
else:
pilOutputImage = Image.fromarray(NPAImageInt, 'L')
if (self.autocontrast is not None):
pilOutputImage = ImageOps.autocontrast(pilOutputImage,
self.autocontrast)
if (self.width is not None) or (self.height is not None):
if (self.width > 0) and (self.height > 0):
if self.keepRatio is True:
# PIL takes care of the ratio
pilOutputImage.thumbnail((self.width, self.height),
Image.ANTIALIAS)
else:
pilOutputImage = pilOutputImage.resize(
(self.width, self.height), Image.ANTIALIAS)
else:
if self.width is None:
pilOutputImage.thumbnail((self.height, self.height),
Image.ANTIALIAS)
elif self.height is None:
pilOutputImage.thumbnail((self.width, self.width),
Image.ANTIALIAS)
if self.invert == True:
pilOutputImage = ImageOps.invert(pilOutputImage)
if self.colorize == True:
pilOutputImage.putpalette(EDPluginExecThumbnailv10.getPalette())
pilOutputImage = pilOutputImage.convert("RGB")
self.synchronizeOn()
if self.format == "jpg":
self.width, self.height = pilOutputImage.size
if self.width * self.height > ImageFile.MAXBLOCK:
ImageFile.MAXBLOCK = self.width * self.height
try:
pilOutputImage.save(self.output,
"JPEG",
quality=85,
optimize=True)
except TypeError:
pilOutputImage.save(self.output)
else:
pilOutputImage.save(self.output)
self.synchronizeOff()
sys.exit(1)
for strPath in listPaths:
EDVerbose.screen("Starting EDNA AutoProc -> ISPyB for file %s" %
strPath)
xsDataInputStoreAutoProc = XSDataInputStoreAutoProc()
strXMLAutoProcContainer = EDUtilsFile.readFile(strPath)
xsDataAutoProcContainer = AutoProcContainer.parseString(
strXMLAutoProcContainer)
if xsDataAutoProcContainer is None:
EDVerbose.WARNING("Couldn't parse file %s" % strPath)
else:
if xsDataAutoProcContainer.AutoProcProgramContainer.AutoProcProgram.processingStatus == "True":
xsDataAutoProcContainer.AutoProcProgramContainer.AutoProcProgram.processingStatus = "SUCCESS"
xsDataInputStoreAutoProc.setAutoProcContainer(
xsDataAutoProcContainer)
edPluginISPyBStoreAutoProc = EDFactoryPluginStatic.loadPlugin(
"EDPluginISPyBStoreAutoProcv1_4")
edPluginISPyBStoreAutoProc.setDataInput(xsDataInputStoreAutoProc)
edPluginISPyBStoreAutoProc.executeSynchronous()
if edPluginISPyBStoreAutoProc.isFailure():
EDVerbose.ERROR("XML data not stored in ISPyB")
else:
xsDataResultISPyBStoreAutoProc = edPluginISPyBStoreAutoProc.dataOutput
EDVerbose.screen("XML data sucessfully stored in ISPyB")
if xsDataResultISPyBStoreAutoProc.autoProcScalingId is not None:
EDVerbose.screen(
"autoProcScalingId: %d" %
xsDataResultISPyBStoreAutoProc.autoProcScalingId.value)
else:
EDVerbose.warning("No autoProcScalingId in results!")
def readHeaderMarccd(self, _strFileName):
"""
Returns an dictionary with the contents of a MAR CCD image header.
"""
#
# Created by Krister Larsson on 08/11/5.
# Modified by Olof Svensson 20090401
#
strUint32 = 'I'
strChar = 's'
#strInt16 = 'H'
strInt32 = 'i'
iMAXIMAGES = 9
pyListHeader = [
#File/header format parameters (256bytes)
[strUint32, 'header_type'],
[strChar, 'header_name', 16],
[strUint32, 'header_major_version'],
[strUint32, 'header_minor_version'],
[strUint32, 'header_byte_order'],
[strUint32, 'data_byte_order'],
[strUint32, 'header_size'],
[strUint32, 'frame_type'],
[strUint32, 'magic_number'],
[strUint32, 'compression_type'],
[strUint32, 'compression1'],
[strUint32, 'compression2'],
[strUint32, 'compression3'],
[strUint32, 'compression4'],
[strUint32, 'compression5'],
[strUint32, 'compression6'],
[strUint32, 'nheaders'],
[strUint32, 'nfast'],
[strUint32, 'nslow'],
[strUint32, 'depth'],
[strUint32, 'record_length'],
[strUint32, 'signif_bits'],
[strUint32, 'data_type'],
[strUint32, 'saturated_value'],
[strUint32, 'sequence'],
[strUint32, 'nimages'],
[strUint32, 'origin'],
[strUint32, 'orientation'],
[strUint32, 'view_direction'],
[strUint32, 'overflow_direction'],
[strUint32, 'over_8_bits'],
[strUint32, 'over_16_bits'],
[strUint32, 'multiplexed'],
[strUint32, 'nfastimages'],
[strUint32, 'nslowimages'],
[strUint32, 'darkcurrent_applied'],
[strUint32, 'bias_applied'],
[strUint32, 'flatfield_applied'],
[strUint32, 'distortion_applied'],
[strUint32, 'original_header_type'],
[strUint32, 'file_saved'],
[strUint32, 'n_valid_pixels'],
[strUint32, 'defectmap_applied'],
[strUint32, 'subimage_nfast'],
[strUint32, 'subimage_nslow'],
[strUint32, 'subimage_origin_fast'],
[strUint32, 'subimage_origin_slow'],
[strUint32, 'readout_pattern'],
[strUint32, 'saturation_level'],
[strUint32, 'orientation_code'],
[strUint32, 'frameshift_multiplexed'],
[strUint32, 'precsan_nfast'],
[strUint32, 'prescan_nslow'],
[strUint32, 'postscan_nfast'],
[strUint32, 'postscan_nslow'],
[strUint32, 'prepost_trimmed'],
[strChar, 'reserve1', 20],
#Data statistics (128 bytes)
[strUint32, 'total_counts', 2],
[strUint32, 'special_counts1', 2],
[strUint32, 'special_counts2', 2],
[strUint32, 'min'],
[strUint32, 'max'],
[strUint32, 'mean'],
[strUint32, 'rms'],
[strUint32, 'n_zeros'],
[strUint32, 'n_saturated'],
[strUint32, 'stats_uptodate'],
[strUint32, 'pixel_noise', iMAXIMAGES],
[strChar, 'reserve2', (19 - iMAXIMAGES) * 4],
#More statistics (256 bytes)
#[uint16,'percentile',128],
#Percentile is substituted by Sample changer info
[strChar, 'barcode', 16],
[strUint32, 'barcode_angle'],
[strUint32, 'barcode_status'],
[strChar, 'reserve2a', 232],
#Goniostat parameters (128 bytes)
[strInt32, 'xtal_to_detector'],
[strInt32, 'beam_x'],
[strInt32, 'beam_y'],
[strInt32, 'integration_time'],
[strInt32, 'exposure_time'],
[strInt32, 'readout_time'],
[strInt32, 'nreads'],
[strInt32, 'start_twotheta'],
[strInt32, 'start_omega'],
[strInt32, 'start_chi'],
[strInt32, 'start_kappa'],
[strInt32, 'start_phi'],
[strInt32, 'start_delta'],
[strInt32, 'start_gamma'],
[strInt32, 'start_xtal_to_detector'],
[strInt32, 'end_twotheta'],
[strInt32, 'end_omega'],
[strInt32, 'end_chi'],
[strInt32, 'end_kappa'],
[strInt32, 'end_phi'],
[strInt32, 'end_delta'],
[strInt32, 'end_gamma'],
[strInt32, 'end_xtal_to_detector'],
[strInt32, 'rotation_axis'],
[strInt32, 'rotation_range'],
[strInt32, 'detector_rotx'],
[strInt32, 'detector_roty'],
[strInt32, 'detector_rotz'],
[strInt32, 'total_dose'],
[strChar, 'reserve3', 12],
#Detector parameters (128 bytes)
[strInt32, 'detector_type'],
[strInt32, 'pixelsize_x'],
[strInt32, 'pixelsize_y'],
[strInt32, 'mean_bias'],
[strInt32, 'photons_per_100adu'],
[strInt32, 'measured_bias', iMAXIMAGES],
[strInt32, 'measured_temperature', iMAXIMAGES],
[strInt32, 'measured_pressure', iMAXIMAGES],
#X-ray source and optics parameters (128 bytes)
[strInt32, 'source_type'],
[strInt32, 'source_dx'],
[strInt32, 'source_dy'],
[strInt32, 'source_wavelength'],
[strInt32, 'source_power'],
[strInt32, 'source_voltage'],
[strInt32, 'source_current'],
[strInt32, 'source_bias'],
[strInt32, 'source_polarization_x'],
[strInt32, 'source_polarization_y'],
[strInt32, 'source_intensity_0'],
[strInt32, 'source_intensity_1'],
[strChar, 'reserve_source', 8],
[strInt32, 'optics_type'],
[strInt32, 'optics_dx'],
[strInt32, 'optics_dy'],
[strInt32, 'optics_wavelength'],
[strInt32, 'optics_dispersion'],
[strInt32, 'optics_crossfire_x'],
[strInt32, 'optics_crossfire_y'],
[strInt32, 'optics_angle'],
[strInt32, 'optics_polarization_x'],
[strInt32, 'optics_polarization_y'],
[strChar, 'reserve_optics', 16],
[strChar, 'reserve5', 16],
#File parameters
[strChar, 'filetitle', 128],
[strChar, 'filepath', 128],
[strChar, 'filename', 64],
[strChar, 'acquire_timestamp', 32],
[strChar, 'header_timestamp', 32],
[strChar, 'save_timestamp', 32],
[strChar, 'file_comment', 512],
[strChar, 'reserve6', 96],
[strChar, 'dataset_comments', 512],
[strChar, 'user_data', 512]
]
pyFile = None
dictMarccd = None
try:
pyFile = open(_strFileName, "rb")
except:
EDVerbose.warning(
"EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: couldn't open file: "
+ _strFileName)
if (pyFile is not None):
EDVerbose.DEBUG(
"EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: Reading header from image "
+ _strFileName)
dictMarccd = {}
#Move to marccd part of header
pyFile.seek(1024)
for pyListRow in pyListHeader:
if len(pyListRow) == 3:
strFormat = str(pyListRow[2]) + str(pyListRow[0])
else:
strFormat = pyListRow[0]
strKeyword = pyListRow[1]
iReadSize = struct.calcsize(strFormat)
pyRawData = pyFile.read(iReadSize)
strValue = struct.unpack(strFormat, pyRawData)
if len(strValue) == 1:
strValue = strValue[0]
if pyListRow[0] == strChar:
strValue = strValue.strip('\x00')
dictMarccd[strKeyword] = strValue
pyFile.close()
return dictMarccd
def getXSDataInputBest(self, _xsDataInputStrategy):
xsDataBeam = _xsDataInputStrategy.getExperimentalCondition().getBeam()
xsDataSample = _xsDataInputStrategy.getSample()
xsDataDetector = _xsDataInputStrategy.getExperimentalCondition(
).getDetector()
xsDataGoniostat = _xsDataInputStrategy.getExperimentalCondition(
).getGoniostat()
xsDataDiffractionPlan = _xsDataInputStrategy.getDiffractionPlan()
xsDataStringBestFileContentDat = _xsDataInputStrategy.getBestFileContentDat(
)
xsDataStringBestFileContentPar = _xsDataInputStrategy.getBestFileContentPar(
)
xsDataFileXdsBackgroundImage = _xsDataInputStrategy.getXdsBackgroundImage(
)
listXSDataStringBestFileContentHKL = _xsDataInputStrategy.getBestFileContentHKL(
)
xsDataInputBest = XSDataInputBest()
# Sample
xsDataAbsorbedDose = None
xsDataSusceptibility = None
# Could be None if sample has not been set
# It could be not None in case Raddose has calculated an absorbed dose with default sample values
if (xsDataSample is not None):
xsDataAbsorbedDose = xsDataSample.getAbsorbedDoseRate()
xsDataSusceptibility = xsDataSample.getSusceptibility()
# crystalShape
# Default value is 1 (We assume that Xtal is smaller than beam)
if xsDataSample.size is not None and xsDataSample.omegaMin is not None:
xsDataInputBest.crystalSize = XSDataSize().parseString(
xsDataSample.size.marshal())
xsDataInputBest.omegaMin = xsDataSample.omegaMin
else:
xsDataDoubleCrystalShape = xsDataSample.getShape()
if (xsDataDoubleCrystalShape is None):
if (xsDataSample.getSize() is
None) or (xsDataBeam.getSize() is None):
xsDataDoubleCrystalShape = XSDataDouble(1)
else:
fCrystalSizeY = xsDataSample.getSize().getY().getValue(
)
fCrystalSizeZ = xsDataSample.getSize().getZ().getValue(
)
fDiagonal = math.sqrt(fCrystalSizeY**2 +
fCrystalSizeZ**2)
fBeamSizeY = xsDataBeam.getSize().getY().getValue()
fCrystalShape = None
if fBeamSizeY > fDiagonal:
fCrystalShape = 1.0
else:
fCrystalShape = int(
10 * fDiagonal / fBeamSizeY) / 10.0
xsDataDoubleCrystalShape = XSDataDouble(fCrystalShape)
xsDataInputBest.setCrystalShape(xsDataDoubleCrystalShape)
# Radiation damage model parameters
xsDataInputBest.setRadiationDamageModelBeta(
xsDataSample.getRadiationDamageModelBeta())
xsDataInputBest.setRadiationDamageModelGamma(
xsDataSample.getRadiationDamageModelGamma())
# Could be None if Raddose failed to calculate the absorbed dose
if (xsDataAbsorbedDose is not None):
xsDataInputBest.setCrystalAbsorbedDoseRate(
xsDataSample.getAbsorbedDoseRate())
xsDataInputBest.setCrystalSusceptibility(xsDataSusceptibility)
# Detector
xsDataInputBest.setDetectorType(xsDataDetector.getType())
# Minimum exposure time per image
xsDataTimeMinExposureTimePerImage = None
if xsDataBeam:
xsDataTimeMinExposureTimePerImage = xsDataBeam.getMinExposureTimePerImage(
)
if xsDataTimeMinExposureTimePerImage == None:
xsDataTimeMinExposureTimePerImage = xsDataDiffractionPlan.getMinExposureTimePerImage(
)
xsDataInputBest.setBeamMinExposureTime(
xsDataTimeMinExposureTimePerImage)
# Max rotation speed
xsDataAngularSpeedMax = None
if xsDataGoniostat:
xsDataAngularSpeedMax = xsDataGoniostat.getMaxOscillationSpeed()
if xsDataDiffractionPlan and xsDataAngularSpeedMax == None:
xsDataAngularSpeedMax = xsDataDiffractionPlan.getGoniostatMaxOscillationSpeed(
)
xsDataInputBest.setGoniostatMaxRotationSpeed(xsDataAngularSpeedMax)
# Min rotation width
xsDataAngleMin = None
if xsDataGoniostat:
xsDataAngleMin = xsDataGoniostat.getMinOscillationWidth()
if xsDataDiffractionPlan and xsDataAngleMin == None:
xsDataAngleMin = xsDataDiffractionPlan.getGoniostatMinOscillationWidth(
)
xsDataInputBest.setGoniostatMinRotationWidth(xsDataAngleMin)
# Other beam parameters
if xsDataBeam:
xsDataInputBest.setBeamExposureTime(xsDataBeam.getExposureTime())
if xsDataBeam.getTransmission():
# Fix for bug 741: if the transmission is zero don't set it and warn the user
fTransmission = xsDataBeam.getTransmission().getValue()
if (abs(fTransmission) < 0.1):
EDVerbose.warning(
"Input transmission to BEST ignored because it is zero or close to zero: %f"
% fTransmission)
else:
xsDataInputBest.setTransmission(
xsDataBeam.getTransmission())
if xsDataBeam.getApertureSize():
xsDataInputBest.setApertureSize(xsDataBeam.getApertureSize())
if xsDataBeam.size:
xsDataInputBest.setBeamSize(xsDataBeam.size)
if xsDataBeam.flux:
xsDataInputBest.setBeamFlux(xsDataBeam.flux)
# Other diffraction plan parameters
if xsDataDiffractionPlan:
xsDataInputBest.setAimedResolution(
xsDataDiffractionPlan.getAimedResolution())
xsDataInputBest.setAimedRedundancy(
xsDataDiffractionPlan.getAimedMultiplicity())
xsDataInputBest.setAimedCompleteness(
xsDataDiffractionPlan.getAimedCompleteness())
xsDataInputBest.setAimedIOverSigma(
xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution())
xsDataInputBest.setBeamMaxExposureTime(
xsDataDiffractionPlan.getMaxExposureTimePerDataCollection())
xsDataInputBest.setComplexity(
xsDataDiffractionPlan.getComplexity())
xsDataInputBest.setAnomalousData(
xsDataDiffractionPlan.getAnomalousData())
xsDataInputBest.setStrategyOption(
xsDataDiffractionPlan.getStrategyOption())
xsDataInputBest.setMinTransmission(
xsDataDiffractionPlan.getMinTransmission())
xsDataInputBest.setNumberOfCrystalPositions(
xsDataDiffractionPlan.getNumberOfPositions())
xsDataInputBest.setDetectorDistanceMin(
xsDataDiffractionPlan.getDetectorDistanceMin())
xsDataInputBest.setDetectorDistanceMax(
xsDataDiffractionPlan.getDetectorDistanceMax())
xsDataInputBest.setUserDefinedRotationStart(
xsDataDiffractionPlan.getUserDefinedRotationStart())
xsDataInputBest.setUserDefinedRotationRange(
xsDataDiffractionPlan.getUserDefinedRotationRange())
xsDataInputBest.doseLimit = xsDataDiffractionPlan.doseLimit
xsDataInputBest.rFriedel = xsDataDiffractionPlan.rFriedel
# Best Files
xsDataInputBest.setBestFileContentDat(xsDataStringBestFileContentDat)
xsDataInputBest.setBestFileContentPar(xsDataStringBestFileContentPar)
xsDataInputBest.setBestFileContentHKL(
listXSDataStringBestFileContentHKL)
xsDataInputBest.setXdsBackgroundImage(xsDataFileXdsBackgroundImage)
return xsDataInputBest
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"]:
print strImageFileNameExtension
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)
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()
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv10.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)
# Raddose is enabled only if the beam flux is set
if(self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None):
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv10.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)
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
# 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)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
strSpaceGroupITNumber = str(self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue())
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()
xsDataRaddoseInput = None
try:
xsDataRaddoseInput = self.__edHandlerXSDataRaddose.getXSDataRaddoseInput(xsDataBeam, self.__xsDataSampleCopy, iNumOperators)
except Exception, detail:
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, self.__edHandlerXSDataRaddose.getClassName() + ": " + str(detail))
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
if(xsDataRaddoseInput is not None):
self.__edPluginRaddose.setDataInput(xsDataRaddoseInput)
self.__edPluginRaddose.setBaseDirectory(self.getWorkingDirectory())
self.__edPluginRaddose.setBaseName(self.__strPluginRaddoseName)
# More checks?
# try:
# self.__edPluginRaddose.setDataInput( xsDataRaddoseInput )
# self.__edPluginRaddose.setBaseDirectory( self.getWorkingDirectory() )
# self.__edPluginRaddose.setBaseName( self.__strPluginRaddoseName )
#
# except Exception, detail:
# warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, str( detail ) )
xsDataBeam = self.getDataInput().getExperimentalCondition(
).getBeam()
xsDataRaddoseInput = None
try:
xsDataRaddoseInput = self.__edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self.__xsDataSampleCopy, iNumOperators)
except Exception, detail:
pyStrWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv1_1.preProcess',
self.__strPluginRaddoseName,
self.__edHandlerXSDataRaddose.getClassName() +
": " + detail)
EDVerbose.warning(pyStrWarningMessage)
self.addWarningMessage(pyStrWarningMessage)
if (xsDataRaddoseInput is not None):
self.__edPluginRaddose.setDataInput(xsDataRaddoseInput)
self.__edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self.__edPluginRaddose.setBaseName(
self.__strPluginRaddoseName)
# More checks?
# try:
# self.__edPluginRaddose.setDataInput( xsDataRaddoseInput )
# self.__edPluginRaddose.setBaseDirectory( self.getWorkingDirectory() )
# self.__edPluginRaddose.setBaseName( self.__strPluginRaddoseName )
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.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)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput().getExperimentalCondition().getBeam().getFlux()
is None):
pyStrWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv1_1.preProcess',
self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(pyStrWarningMessage)
self.addWarningMessage(pyStrWarningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(
self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.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)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
# 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)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self.__xsDataSampleCopy.getCrystal(
xsDataBeam = self.getDataInput().getExperimentalCondition(
).getBeam()
xsDataRaddoseInput = None
try:
xsDataRaddoseInput = self.__edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self.__xsDataSampleCopy, iNumOperators)
except Exception, detail:
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv10.preProcess',
self.__strPluginRaddoseName,
self.__edHandlerXSDataRaddose.getClassName() + ": " +
str(detail))
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
if (xsDataRaddoseInput is not None):
self.__edPluginRaddose.setDataInput(xsDataRaddoseInput)
self.__edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self.__edPluginRaddose.setBaseName(
self.__strPluginRaddoseName)
# More checks?
# try:
# self.__edPluginRaddose.setDataInput( xsDataRaddoseInput )
# self.__edPluginRaddose.setBaseDirectory( self.getWorkingDirectory() )
# self.__edPluginRaddose.setBaseName( self.__strPluginRaddoseName )
#
