def saveModuleDictionaryToDisk(self, _strPath):
"""
This method saves the module dictionary to disk in form of XML.
This method should be private but is kept public in order to be unit tested.
@param _strPath: Path to the module dictionary XML file
@type _strPath: python string
"""
xsDataDictionaryPlugin = XSDataDictionary()
strEdnaHome = EDUtilsPath.EDNA_HOME
for strModule in self.__dictModuleLocation:
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(XSDataString(strModule))
strModuleLocation = self.__dictModuleLocation[strModule]
# Remove the path up to $EDNA_HOME
strModuleLocationStripped = strModuleLocation.replace(
strEdnaHome, "")
if (strModuleLocationStripped.startswith("/")
or strModuleLocationStripped.startswith("\\")):
strModuleLocationStripped = strModuleLocationStripped[1:]
xsDataKeyValuePair.setValue(
XSDataString(strModuleLocationStripped))
xsDataDictionaryPlugin.addKeyValuePair(xsDataKeyValuePair)
try:
xsDataDictionaryPlugin.exportToFile(_strPath)
except Exception:
self.warning("The module cache could not be written to disk.")
def saveModuleDictionaryToDisk(self, _strPath):
"""
This method saves the module dictionary to disk in form of XML.
This method should be private but is kept public in order to be unit tested.
@param _strPath: Path to the module dictionary XML file
@type _strPath: python string
"""
xsDataDictionaryPlugin = XSDataDictionary()
strEdnaHome = EDUtilsPath.EDNA_HOME
for strModule in self.__dictModuleLocation:
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(XSDataString(strModule))
strModuleLocation = self.__dictModuleLocation[ strModule ]
# Remove the path up to $EDNA_HOME
strModuleLocationStripped = strModuleLocation.replace(strEdnaHome, "")
if (strModuleLocationStripped.startswith("/") or strModuleLocationStripped.startswith("\\")):
strModuleLocationStripped = strModuleLocationStripped[1:]
xsDataKeyValuePair.setValue(XSDataString(strModuleLocationStripped))
xsDataDictionaryPlugin.addKeyValuePair(xsDataKeyValuePair)
try:
xsDataDictionaryPlugin.exportToFile(_strPath)
except:
self.warning("The module cache could not be written to disk.")
def createOutputFileDictionary(self, _xsDataResultCharacterisation, _strPathToLogFileDirectory=None):
"""
This method creates an XSDataDictionary containing the name and locations of the
characterisation output files.
"""
xsDataDictionaryLogFile = XSDataDictionary()
# Start with the prediction images
xsDataIndexingResult = _xsDataResultCharacterisation.getIndexingResult()
if xsDataIndexingResult is not None:
xsDataGeneratePredictionResult = xsDataIndexingResult.getPredictionResult()
if xsDataGeneratePredictionResult is not None:
listXSDataImagePrediction = xsDataGeneratePredictionResult.getPredictionImage()
for xsDataImagePrediction in listXSDataImagePrediction:
xsDataKeyValuePair = XSDataKeyValuePair()
iPredictionImageNumber = xsDataImagePrediction.getNumber().getValue()
xsDataStringKey = XSDataString("predictionImage_%d" % iPredictionImageNumber)
xsDataStringValue = None
strPredictionImagePath = xsDataImagePrediction.getPath().getValue()
if (_strPathToLogFileDirectory is not None):
strPredictionImageFileName = EDUtilsFile.getBaseName(strPredictionImagePath)
strNewPredictionImagePath = os.path.join(_strPathToLogFileDirectory, strPredictionImageFileName)
EDUtilsFile.copyFile(strPredictionImagePath, strNewPredictionImagePath)
xsDataStringValue = XSDataString(strNewPredictionImagePath)
else:
xsDataStringValue = XSDataString(strPredictionImageFileName)
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
# Best log file
strPathToBESTLogFile = None
strPathToExecutiveSummary = None
if _xsDataResultCharacterisation.getStrategyResult() is not None:
if _xsDataResultCharacterisation.getStrategyResult().getBestLogFile() != None:
strPathToBESTLogFile = _xsDataResultCharacterisation.getStrategyResult().getBestLogFile().getPath().getValue()
if strPathToBESTLogFile is not None:
xsDataStringKey = XSDataString("logFileBest")
xsDataStringValue = None
if (_strPathToLogFileDirectory is not None):
strNewBestLogPath = os.path.join(_strPathToLogFileDirectory, "best.log")
EDUtilsFile.copyFile(strPathToBESTLogFile, strNewBestLogPath)
xsDataStringValue = XSDataString(strNewBestLogPath)
else:
xsDataStringValue = XSDataString(strPathToBESTLogFile)
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
if (strPathToExecutiveSummary is not None):
xsDataStringKey = XSDataString("executiveSummary")
xsDataStringValue = None
if (_strPathToLogFileDirectory is not None):
strExecutiveSummaryFileName = EDUtilsFile.getBaseName(strPathToExecutiveSummary)
strNewExecutiveSummaryPath = os.path.join(_strPathToLogFileDirectory, strExecutiveSummaryFileName)
EDUtilsFile.copyFile(strPathToExecutiveSummary, strNewExecutiveSummaryPath)
xsDataStringValue = XSDataString(strNewExecutiveSummaryPath)
# Copy also the executive summary file to "dna_log.txt"...
strNewExecutiveSummaryPath = os.path.join(_strPathToLogFileDirectory, "dna_log.txt")
EDUtilsFile.copyFile(strPathToExecutiveSummary, strNewExecutiveSummaryPath)
else:
xsDataStringValue = XSDataString(strPathToExecutiveSummary)
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
return xsDataDictionaryLogFile
def createOutputFileDictionary(self,
_xsDataResultCharacterisation,
_strPathToLogFileDirectory=None):
"""
This method creates an XSDataDictionary containing the name and locations of the
characterisation output files.
"""
xsDataDictionaryLogFile = XSDataDictionary()
# Start with the prediction images
xsDataIndexingResult = _xsDataResultCharacterisation.getIndexingResult(
)
xsDataGeneratePredictionResult = xsDataIndexingResult.getPredictionResult(
)
listXSDataImagePrediction = xsDataGeneratePredictionResult.getPredictionImage(
)
for xsDataImagePrediction in listXSDataImagePrediction:
xsDataKeyValuePair = XSDataKeyValuePair()
iPredictionImageNumber = xsDataImagePrediction.getNumber(
).getValue()
xsDataStringKey = XSDataString("predictionImage_%d" %
iPredictionImageNumber)
xsDataStringValue = None
strPredictionImagePath = xsDataImagePrediction.getPath().getValue()
if (_strPathToLogFileDirectory is not None):
strPredictionImageFileName = EDUtilsFile.getBaseName(
strPredictionImagePath)
strNewPredictionImagePath = os.path.join(
_strPathToLogFileDirectory, strPredictionImageFileName)
EDUtilsFile.copyFile(strPredictionImagePath,
strNewPredictionImagePath)
xsDataStringValue = XSDataString(strNewPredictionImagePath)
else:
xsDataStringValue = XSDataString(strPredictionImageFileName)
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
# Best log file
strPathToBESTLogFile = None
strPathToExecutiveSummary = None
if _xsDataResultCharacterisation.getStrategyResult().getBestLogFile(
) != None:
strPathToBESTLogFile = _xsDataResultCharacterisation.getStrategyResult(
).getBestLogFile().getPath().getValue()
if strPathToBESTLogFile is not None:
xsDataStringKey = XSDataString("logFileBest")
xsDataStringValue = None
if (_strPathToLogFileDirectory is not None):
strNewBestLogPath = os.path.join(_strPathToLogFileDirectory,
"best.log")
EDUtilsFile.copyFile(strPathToBESTLogFile, strNewBestLogPath)
xsDataStringValue = XSDataString(strNewBestLogPath)
else:
xsDataStringValue = XSDataString(strPathToBESTLogFile)
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
if (strPathToExecutiveSummary is not None):
xsDataStringKey = XSDataString("executiveSummary")
xsDataStringValue = None
if (_strPathToLogFileDirectory is not None):
strExecutiveSummaryFileName = EDUtilsFile.getBaseName(
strPathToExecutiveSummary)
strNewExecutiveSummaryPath = os.path.join(
_strPathToLogFileDirectory, strExecutiveSummaryFileName)
EDUtilsFile.copyFile(strPathToExecutiveSummary,
strNewExecutiveSummaryPath)
xsDataStringValue = XSDataString(strNewExecutiveSummaryPath)
# Copy also the executive summary file to "dna_log.txt"...
strNewExecutiveSummaryPath = os.path.join(
_strPathToLogFileDirectory, "dna_log.txt")
EDUtilsFile.copyFile(strPathToExecutiveSummary,
strNewExecutiveSummaryPath)
else:
xsDataStringValue = XSDataString(strPathToExecutiveSummary)
xsDataKeyValuePair = XSDataKeyValuePair()
xsDataKeyValuePair.setKey(xsDataStringKey)
xsDataKeyValuePair.setValue(xsDataStringValue)
xsDataDictionaryLogFile.addKeyValuePair(xsDataKeyValuePair)
return xsDataDictionaryLogFile
def doSuccessExecNormalize(self, _edPlugin=None):
with self.locked():
self.DEBUG(
"EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlFullFieldXASv1_0.doSuccessExecNormalize")
self.xsdAlignStack.setMeasureOffset(self.xsdMeasureOffset)
output = _edPlugin.dataOutput.output
self.xsdAlignStack.images = [output]
data = EDUtilsArray.getArray(output)
data.shape = -1
self.xsdAlignStack.index = [XSDataInteger(self.index)]
self.xsdAlignStack.frameReference = XSDataInteger(self.reference)
self.xsdAlignStack.HDF5File = self.dataInput.getHDF5File()
self.xsdAlignStack.internalHDF5Path = self.internalHDF5Path
internalHDF5Path = self.internalHDF5Path.value
if not internalHDF5Path.startswith("/"):
internalHDF5Path = "/" + internalHDF5Path
keyValuePair1 = XSDataKeyValuePair(key=XSDataString("axes"),
value=XSDataString(
self.DSenergy))
keyValuePair2 = XSDataKeyValuePair(key=XSDataString("long_name"),
value=XSDataString(self.TITLE))
keyValuePair3 = XSDataKeyValuePair(
key=XSDataString("interpretation"),
value=XSDataString("image"))
keyValuePair4 = XSDataKeyValuePair(key=XSDataString("signal"),
value=XSDataString("1"))
xsAttrDataset = XSDataHDF5Attributes(
h5path=XSDataString(
posixpath.join(internalHDF5Path, self.DSstack)),
metadata=XSDataDictionary([
XSDataKeyValuePair(key=XSDataString(k),
value=XSDataString(v))
for k, v in self.dataAttr.items()
]))
# NXdata is treated in this file not in HDF5 plugins
# xsAttrNXdata = XSDataHDF5Attributes(h5path=XSDataString(posixpath.join(internalHDF5Path, "NXdata")), \
# metadata=XSDataDictionary([XSDataKeyValuePair(key=XSDataString(k), value=XSDataString(v)) for k, v in self.NXdataAttr.items()]))
xsAttrEntry = XSDataHDF5Attributes(
h5path=XSDataString(internalHDF5Path),
metadata=XSDataDictionary([
XSDataKeyValuePair(key=XSDataString(k),
value=XSDataString(v))
for k, v in self.NXentryAttr.items()
]))
self.xsdAlignStack.extraAttributes = [xsAttrDataset, xsAttrEntry]
########################################################################
# Selecte the mean of last centile
########################################################################
data.sort()
fMaxSignal = data[int(0.99 * len(data)):].mean()
self.makeHDF5MaxIntStructure(fMaxSignal)