def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(
self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile(
).getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(
strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile] = (
self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(
self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(
XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) *
int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(
self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" %
strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputID11)
self.bTimedOut = False
self.__dictID11 = {}
self.__strControlledPluginWait = "EDPluginWaitMultiFile"
self.__edPluginWaitMultipleFile = None
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
self.__listProcessedFiles = []
self.__strControlledPluginSPD = "EDPluginSPDCakev1_5"
self.__xsDataInputSPDCake = None
self.__strControlledPluginEDF = "EDPluginExportAsciiPowderv1_0"
self.bCorrectMask = True
def testCheckParameters(self):
xsDataInput = XSDataInputWaitMultiFile()
xsDataInput.setExpectedFile([XSDataFile(XSDataString("toto"))])
xsDataInput.setExpectedSize(XSDataInteger(10))
edPluginWaitMultiFile = self.createPlugin()
edPluginWaitMultiFile.setDataInput(xsDataInput)
edPluginWaitMultiFile.checkParameters()
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputID11)
self.bTimedOut = False
self.__dictID11 = {}
self.__strControlledPluginWait = "EDPluginWaitMultiFile"
self.__edPluginWaitMultipleFile = None
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
self.__listProcessedFiles = []
self.__strControlledPluginSPD = "EDPluginSPDCakev1_5"
self.__xsDataInputSPDCake = None
self.__strControlledPluginEDF = "EDPluginExportAsciiPowderv1_0"
self.bCorrectMask = True
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginBioSaxsAveragev1_0.process")
xsdiWaitMultiFile = XSDataInputWaitMultiFile(
expectedFile=[
XSDataFile(i.path) for i in self.dataInput.integratedImage
],
expectedSize=self.dataInput.integratedImageSize,
timeOut=XSDataTime(30))
self.__edPluginWaitMultiFile.setDataInput(xsdiWaitMultiFile)
self.__edPluginWaitMultiFile.connectSUCCESS(
self.doSuccessWaitMultiFile)
self.__edPluginWaitMultiFile.connectFAILURE(
self.doFailureWaitMultiFile)
self.__edPluginWaitMultiFile.executeSynchronous()
def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
def preProcess(self, _edPlugin=None):
"""
Prepares the execution plugin
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlImageQualityIndicatorsv1_1.preProcess...")
# List containing instances of all the exeuction plugins
self.listPluginExecImageQualityIndicator = []
# Loop through all the incoming reference images
self.edPluginWaitMultiFile = self.loadPlugin(self.strPluginExecWaitMultiFileName)
listXSDataImage = self.getDataInput().getImage()
xsDataInputWaitMultiFile = XSDataInputWaitMultiFile()
for xsDataImage in listXSDataImage:
xsDataInputWaitMultiFile.addExpectedFile(XSDataFile(xsDataImage.getPath()))
xsDataInputWaitMultiFile.setExpectedSize(XSDataInteger(100000))
xsDataInputWaitMultiFile.setTimeOut(XSDataTime(self.fWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fWaitFileTimeOut)
self.edPluginWaitMultiFile.setDataInput(xsDataInputWaitMultiFile)
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile().getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile] = (self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) * int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" % strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_3.process")
xsdwf = XSDataInputWaitMultiFile(timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist"%dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist"%inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity is not None):
if self.absoluteFidelity is not None :
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" % (idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity) and (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None) :
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None) :
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.lstSummary.append("WARNING: " + self.strRadiationDamage)
self.lstSummary.append("Merging files: " + " ".join([os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value, self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
#outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(self.__strControlledPluginAutoSub)
base = "_".join(os.path.basename(self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile), base + "_" + suff)
xsd = XSDataInputAutoSub(sampleCurve=self.__class__.lastSample,
buffers=[self.__class__.lastBuffer, self.dataInput.mergedCurve],
subtractedCurve=XSDataFile(XSDataString(sub))
)
self.__edPluginExecAutoSub.setDataInput(xsd)
self.__edPluginExecAutoSub.connectSUCCESS(self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
self.__class__.lastSample = None
else:
self.__class__.lastSample = self.dataInput.mergedCurve
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_1.process")
xsdwf = XSDataInputWaitMultiFile(timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
shutil.copyfile(self.lstInput[0].path.value, self.dataInput.mergedCurve.path.value)
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity is not None):
if self.absoluteFidelity is not None :
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" % (idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity) and (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None) :
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None) :
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
if (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.lstSummary.append("WARNING: " + self.strRadiationDamage)
self.lstSummary.append("Merging files: " + " ".join([os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
shutil.copyfile(self.lstMerged[0].path.value, self.dataInput.mergedCurve.path.value)
else:
self.__edPluginExecDataver = self.loadPlugin(self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
#outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if self.isFailure():
return
self.__edPluginExecAutoRg = self.loadPlugin(self.__strControlledPluginAutoRG)
xsd = XSDataInputAutoRg(inputCurve=[self.dataInput.mergedCurve])
self.__edPluginExecAutoRg.setDataInput(xsd)
self.__edPluginExecAutoRg.connectSUCCESS(self.doSuccessExecAutoRg)
self.__edPluginExecAutoRg.connectFAILURE(self.doFailureExecAutoRg)
self.__edPluginExecAutoRg.executeSynchronous()
class EDPluginControlID11v1_0(EDPluginControl):
"""
Plugin specific to ID11
"""
__semaphore = threading.Semaphore()
__dictParamID11XSD = {} #key=filename, value=(dictID11,strXSD
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputID11)
self.bTimedOut = False
self.__dictID11 = {}
self.__strControlledPluginWait = "EDPluginWaitMultiFile"
self.__edPluginWaitMultipleFile = None
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
self.__listProcessedFiles = []
self.__strControlledPluginSPD = "EDPluginSPDCakev1_5"
self.__xsDataInputSPDCake = None
self.__strControlledPluginEDF = "EDPluginExportAsciiPowderv1_0"
self.bCorrectMask = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlID11v1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getParameterFile(), "No parameter file!")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile().getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile] = (self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) * int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" % strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlID11v1_0.process")
self.__edPluginWaitMultipleFile.connectSUCCESS(self.doSuccessExecWaitMultipleFile)
self.__edPluginWaitMultipleFile.connectFAILURE(self.doFailureExecWaitMultipleFile)
self.__edPluginWaitMultipleFile.executeSynchronous()
# SPD launch
if self.bTimedOut:
self.ERROR("EDPluginControlID11v1_0.process: Wait Multi File ended in Timeout")
self.setFailure()
return
for onefile in self.getDataInput().getDataFile():
self.synchronizeOn()
edPluginSPD = self.loadPlugin(self.__strControlledPluginSPD)
self.__xsDataInputSPDCake.setInputFile(onefile)
edPluginSPD.setDataInput(self.__xsDataInputSPDCake)
edPluginSPD.connectSUCCESS(self.doSuccessExecSPDCake)
edPluginSPD.connectFAILURE(self.doFailureExecSPDCake)
edPluginSPD.execute()
self.synchronizeOff()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlID11v1_0.postProcess")
#Wait for all plugins to finish
self.synchronizePlugins()
# Create some output data
xsDataResult = XSDataResultID11()
xsDataResult.setOutputFile(self.__listProcessedFiles)
self.setDataOutput(xsDataResult)
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT" in self.__dictID11) and (self.__dictID11["DARK CURRENT"] == "YES") :
if ("DC FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"] == "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning("Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"] == "YES") :
if ("MASK FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"] == "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning("Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !" % (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(XSDataDouble(1 / value))
else:
self.warning("Asked for FF SCALE correction but no FF MULTIPLIER provided")
if ("SPATIAL DIS." in self.__dictID11) and (self.__dictID11["SPATIAL DIS."] == "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else :
self.warning("Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file")
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue((float(self.__dictID11["END AZIMUTH"]) - float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def parseParameterFiles(self, _strPath):
"""
parses Configuration file
"""
self.DEBUG("EDPluginControlID11v1_0.parseParameterFiles")
self.__dictID11 = {}
dictSub = {"${TEST_DATA_IMAGES_HOME}": EDUtilsTest.getTestsDataImagesHome()}
for linefile in EDUtilsFile.readFileAndParseVariables(_strPath, dictSub).split("\n"):
strLineData = linefile.strip()
#discard comment lines
if not strLineData.startswith('#') :
# discard end line carriage return
splited = strLineData.split("=", 1)
if len(splited) == 2:
self.__dictID11[splited[0].strip()] = splited[1].strip()
return self.__dictID11
def doSuccessExecWaitMultipleFile(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doSuccessExecWaitMultipleFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID11v1_0.doSuccessExecWaitMultipleFile")
xsDataResult = self.__edPluginWaitMultipleFile.getDataOutput()
self.bTimedOut = xsDataResult.getTimedOut().getValue()
# self.screen("got TimeOut=%s Type is %s" % (self.bTimedOut, type(self.bTimedOut)))
def doFailureExecWaitMultipleFile(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doFailureExecWaitMultipleFile")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlID11v1_0.doFailureExecWaitMultipleFile")
self.setFailure()
def doSuccessExecSPDCake(self, _edPlugin=None):
self.synchronizeOn()
self.DEBUG("EDPluginControlID11v1_0.doSuccessExecSPDCake")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID11v1_0.doSuccessExecSPDCake")
xsdOut = _edPlugin.getDataOutput()
xsdAzimFile = xsdOut.getCakedFile()
xsdIn = XSDataInput1DPowderEDF()
xsdIn.setEdfFile(xsdAzimFile)
strInputFile = os.path.basename(_edPlugin.getDataInput().getInputFile().getPath().getValue())
xsdFile = XSDataFile()
xsdFile.setPath(XSDataString(
os.path.join(self.__dictID11["output_dir"], os.path.splitext(strInputFile)[0] + "." + self.__dictID11["output_extn"])
))
xsdIn.setOutputFile(xsdFile)
xsdIn.setEdfFile(xsdOut.getCakedFile())
xsdIn.setOutputFormat(XSDataString(self.__dictID11["output_extn"]))
xsdIn.setNumberOfBins(XSDataInteger(int(self.__dictID11["RADIAL BINS"])))
# EDF Launch
edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
edPluginEDF.setDataInput(xsdIn)
edPluginEDF.connectSUCCESS(self.doSuccessExec1DPowderEDF)
edPluginEDF.connectFAILURE(self.doFailureExec1DPowderEDF)
edPluginEDF.execute()
self.synchronizeOff()
def doFailureExecSPDCake(self, _edPlugin=None):
self.synchronizeOn()
self.DEBUG("EDPluginControlID11v1_0.doFailureExecSPDCake")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlID11v1_0.doFailureExecSPDCake")
xsd = _edPlugin.getDataInput()
if xsd is not None:
filename = xsd.getInputFile().getPath().getValue()
self.ERROR("SPD ended in error with file %s" % filename)
else:
self.ERROR("SPD ended in error with no input data (!!!!)")
self.setFailure()
self.synchronizeOff()
def doSuccessExec1DPowderEDF(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doSuccessExec1DPowderEDF")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID11v1_0.doSuccessExec1DPowderEDF")
self.synchronizeOn()
self.__listProcessedFiles.append(_edPlugin.getDataOutput().getOutputFile())
self.synchronizeOff()
def doFailureExec1DPowderEDF(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doFailureExec1DPowderEDF")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlID11v1_0.doFailureExec1DPowderEDF")
self.setFailure()
class EDPluginControlID11v1_0(EDPluginControl):
"""
Plugin specific to ID11
"""
__semaphore = threading.Semaphore()
__dictParamID11XSD = {} #key=filename, value=(dictID11,strXSD
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputID11)
self.bTimedOut = False
self.__dictID11 = {}
self.__strControlledPluginWait = "EDPluginWaitMultiFile"
self.__edPluginWaitMultipleFile = None
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
self.__listProcessedFiles = []
self.__strControlledPluginSPD = "EDPluginSPDCakev1_5"
self.__xsDataInputSPDCake = None
self.__strControlledPluginEDF = "EDPluginExportAsciiPowderv1_0"
self.bCorrectMask = True
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginControlID11v1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getParameterFile(),
"No parameter file!")
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(
self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile(
).getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(
strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile] = (
self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(
self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(
XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) *
int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(
self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" %
strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlID11v1_0.process")
self.__edPluginWaitMultipleFile.connectSUCCESS(
self.doSuccessExecWaitMultipleFile)
self.__edPluginWaitMultipleFile.connectFAILURE(
self.doFailureExecWaitMultipleFile)
self.__edPluginWaitMultipleFile.executeSynchronous()
# SPD launch
if self.bTimedOut:
self.ERROR(
"EDPluginControlID11v1_0.process: Wait Multi File ended in Timeout"
)
self.setFailure()
return
for onefile in self.getDataInput().getDataFile():
self.synchronizeOn()
edPluginSPD = self.loadPlugin(self.__strControlledPluginSPD)
self.__xsDataInputSPDCake.setInputFile(onefile)
edPluginSPD.setDataInput(self.__xsDataInputSPDCake)
edPluginSPD.connectSUCCESS(self.doSuccessExecSPDCake)
edPluginSPD.connectFAILURE(self.doFailureExecSPDCake)
edPluginSPD.execute()
self.synchronizeOff()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlID11v1_0.postProcess")
#Wait for all plugins to finish
self.synchronizePlugins()
# Create some output data
xsDataResult = XSDataResultID11()
xsDataResult.setOutputFile(self.__listProcessedFiles)
self.setDataOutput(xsDataResult)
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(
self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(
self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT"
in self.__dictID11) and (self.__dictID11["DARK CURRENT"]
== "YES"):
if ("DC FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"]
== "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning(
"Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"]
== "YES"):
if ("MASK FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"]
== "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning(
"Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !"
% (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(
XSDataDouble(1 / value))
else:
self.warning(
"Asked for FF SCALE correction but no FF MULTIPLIER provided"
)
if ("SPATIAL DIS."
in self.__dictID11) and (self.__dictID11["SPATIAL DIS."]
== "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else:
self.warning(
"Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file"
)
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(
self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue(
(float(self.__dictID11["END AZIMUTH"]) -
float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(
XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def parseParameterFiles(self, _strPath):
"""
parses Configuration file
"""
self.DEBUG("EDPluginControlID11v1_0.parseParameterFiles")
self.__dictID11 = {}
dictSub = {
"${TEST_DATA_IMAGES_HOME}": EDUtilsTest.getTestsDataImagesHome()
}
for linefile in EDUtilsFile.readFileAndParseVariables(
_strPath, dictSub).split("\n"):
strLineData = linefile.strip()
#discard comment lines
if not strLineData.startswith('#'):
# discard end line carriage return
splited = strLineData.split("=", 1)
if len(splited) == 2:
self.__dictID11[splited[0].strip()] = splited[1].strip()
return self.__dictID11
def doSuccessExecWaitMultipleFile(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doSuccessExecWaitMultipleFile")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlID11v1_0.doSuccessExecWaitMultipleFile")
xsDataResult = self.__edPluginWaitMultipleFile.getDataOutput()
self.bTimedOut = xsDataResult.getTimedOut().getValue()
# self.screen("got TimeOut=%s Type is %s" % (self.bTimedOut, type(self.bTimedOut)))
def doFailureExecWaitMultipleFile(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doFailureExecWaitMultipleFile")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlID11v1_0.doFailureExecWaitMultipleFile")
self.setFailure()
def doSuccessExecSPDCake(self, _edPlugin=None):
self.synchronizeOn()
self.DEBUG("EDPluginControlID11v1_0.doSuccessExecSPDCake")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlID11v1_0.doSuccessExecSPDCake")
xsdOut = _edPlugin.getDataOutput()
xsdAzimFile = xsdOut.getCakedFile()
xsdIn = XSDataInput1DPowderEDF()
xsdIn.setEdfFile(xsdAzimFile)
strInputFile = os.path.basename(
_edPlugin.getDataInput().getInputFile().getPath().getValue())
xsdFile = XSDataFile()
xsdFile.setPath(
XSDataString(
os.path.join(
self.__dictID11["output_dir"],
os.path.splitext(strInputFile)[0] + "." +
self.__dictID11["output_extn"])))
xsdIn.setOutputFile(xsdFile)
xsdIn.setEdfFile(xsdOut.getCakedFile())
xsdIn.setOutputFormat(XSDataString(self.__dictID11["output_extn"]))
xsdIn.setNumberOfBins(
XSDataInteger(int(self.__dictID11["RADIAL BINS"])))
# EDF Launch
edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
edPluginEDF.setDataInput(xsdIn)
edPluginEDF.connectSUCCESS(self.doSuccessExec1DPowderEDF)
edPluginEDF.connectFAILURE(self.doFailureExec1DPowderEDF)
edPluginEDF.execute()
self.synchronizeOff()
def doFailureExecSPDCake(self, _edPlugin=None):
self.synchronizeOn()
self.DEBUG("EDPluginControlID11v1_0.doFailureExecSPDCake")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlID11v1_0.doFailureExecSPDCake")
xsd = _edPlugin.getDataInput()
if xsd is not None:
filename = xsd.getInputFile().getPath().getValue()
self.ERROR("SPD ended in error with file %s" % filename)
else:
self.ERROR("SPD ended in error with no input data (!!!!)")
self.setFailure()
self.synchronizeOff()
def doSuccessExec1DPowderEDF(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doSuccessExec1DPowderEDF")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlID11v1_0.doSuccessExec1DPowderEDF")
self.synchronizeOn()
self.__listProcessedFiles.append(
_edPlugin.getDataOutput().getOutputFile())
self.synchronizeOff()
def doFailureExec1DPowderEDF(self, _edPlugin=None):
self.DEBUG("EDPluginControlID11v1_0.doFailureExec1DPowderEDF")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlID11v1_0.doFailureExec1DPowderEDF")
self.setFailure()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_7.process")
xsdwf = XSDataInputWaitMultiFile(
timeOut=XSDataTime(30),
expectedSize=XSDataInteger(self.minimumCurveFileSize),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist" % dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist" % inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
self.addExecutiveSummaryLine(
"Got only one frame ... nothing to merge !!!")
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity
is not None):
if self.absoluteFidelity is not None:
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
self.datcmp(self.lstInput[0], oneFile)
# edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
# edPluginExecAbsoluteFidelity.setDataInput(xsd)
# edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
self.datcmp(self.lstInput[0], self.lstInput[1])
# edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
# edPluginExecAbsoluteFidelity.setDataInput(xsd)
# edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" %
(idx, idx + 1))
self.datcmp(self.lstInput[idx + 1], oneFile)
# edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
# xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
# edPluginExecRelativeFidelity.setDataInput(xsd)
# edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
# edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
# edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity
is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity) and (self.dictSimilarities[
(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None):
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity):
self.lstMerged.append(oneFile)
elif (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(idx - 1, idx)] >=
self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(
self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.addExecutiveSummaryLine("WARNING: " +
self.strRadiationDamage)
self.addExecutiveSummaryLine("Merging files: " + " ".join(
[os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value,
self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(
self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
# outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(
self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(
self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer
is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(
self.__strControlledPluginAutoSub)
base = "_".join(
os.path.basename(
self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile),
base + "_" + suff)
self.xsdSubtractedCurve = XSDataFile(XSDataString(sub))
#self.curves.append(xsdSubtractedCurve)
self.__edPluginExecAutoSub.dataInput = XSDataInputAutoSub(
sampleCurve=self.__class__.lastSample,
buffers=[
self.__class__.lastBuffer, self.dataInput.mergedCurve
],
subtractedCurve=self.xsdSubtractedCurve)
self.__edPluginExecAutoSub.connectSUCCESS(
self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(
self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
if self.isFailure():
return
self.__edPluginSaxsAnalysis = self.loadPlugin(
self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(
scatterCurve=self.xsdSubtractedCurve,
autoRg=self.autoRg,
graphFormat=XSDataString("png"))
self.__edPluginSaxsAnalysis.connectSUCCESS(
self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(
self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
#self.__class__.lastSample = None #Information neededfor transfer to ISPyB
self.forgetLastSample = True
else:
self.__class__.lastSample = self.dataInput.mergedCurve
if self.dataInput.sample and self.dataInput.sample.login and self.dataInput.sample.passwd and self.dataInput.sample.measurementID:
self.addExecutiveSummaryLine("Registering to ISPyB")
self.lstDiscarded = list(set(self.lstInput) - set(self.lstMerged))
self.__class__.dictFrames[self.dataInput.mergedCurve] = {
'averaged': self.lstMerged,
'discarded': self.lstDiscarded
}
self.__edPluginSaxsISPyB = self.loadPlugin(
self.__strControlledPluginSaxsISPyB)
if len(self.lstInput) > 1:
frameAverage = XSDataInteger(len(self.lstInput))
frameMerged = XSDataInteger(len(self.lstMerged))
else:
frameMerged = frameAverage = XSDataInteger(1)
self.curves = [XSDataFile(i.path) for i in self.lstInput]
self.discardedCurves = [
XSDataFile(i.path) for i in self.lstDiscarded
]
self.mergedCurves = [XSDataFile(i.path) for i in self.lstMerged]
averageFilePath = None
if self.strMergedFile is not None:
averageFilePath = XSDataFile(XSDataString(self.strMergedFile))
self.sampleFrames = self.getAveragedFrameByFilename(
self.__class__.lastSample)
lastSample = None
if self.__class__.lastSample is not None:
lastSample = self.__class__.lastSample
subtractedCurve = None
if self.xsdSubtractedCurve is not None:
subtractedCurve = self.xsdSubtractedCurve
else:
subtractedCurve = None
xsdin = XSDataInputBioSaxsISPyBv1_0(
sample=self.dataInput.sample,
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.volume,
frameAverage=frameAverage,
frameMerged=frameMerged,
curves=self.curves,
discardedFrames=self.discardedCurves,
averagedFrames=self.mergedCurves,
averageFilePath=averageFilePath,
bufferFrames=self.bufferFrames,
sampleFrames=self.sampleFrames,
bestBuffer=self.xsBestBuffer,
averageSample=lastSample,
scatterPlot=self.xsScatterPlot,
guinierPlot=self.xsGuinierPlot,
kratkyPlot=self.xsKratkyPlot,
densityPlot=self.xsDensityPlot,
subtractedFilePath=subtractedCurve
# destination=self.dataInput.sample.ispybDestination #duplicate, already in sample
)
self.__edPluginSaxsISPyB.dataInput = xsdin
self.__edPluginSaxsISPyB.connectSUCCESS(self.doSuccessISPyB)
self.__edPluginSaxsISPyB.connectFAILURE(self.doFailureISPyB)
self.__edPluginSaxsISPyB.execute()
# transfer analysis data to correct location on nice
if self.gnom is not None:
self.outdir = os.path.join(
os.path.dirname(os.path.dirname(self.lstStrInput[0])),
"ednaAnalysis")
basename = os.path.basename(
os.path.splitext(self.gnom.gnomFile.path.value)[0])
self.outdir = os.path.join(self.outdir, basename)
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
#self.outFile = os.path.join(outdir, "NoResults.html")
workingdir = os.path.dirname(self.gnom.gnomFile.path.value)
self.pluginRsync = self.loadPlugin(self.cpRsync)
self.pluginRsync.dataInput = XSDataInputRsync(
source=XSDataFile(XSDataString(workingdir)),
destination=XSDataFile(XSDataString(self.outdir)),
options=XSDataString("-avx"))
self.pluginRsync.connectSUCCESS(self.doSuccessExecRsync)
self.pluginRsync.connectFAILURE(self.doFailureExecRsync)
self.pluginRsync.executeSynchronous()
if self.forgetLastSample:
#Also redefine dictionary to contain the buffer just processed?
self.__class__.lastSample = None
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_0.process")
xsdwf = XSDataInputWaitMultiFile(
timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
# if self.isFailure():
# return
if len(self.lstInput) == 1:
shutil.copyfile(self.lstInput[0].path.value,
self.dataInput.mergedCurve.path.value)
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity
is not None):
if self.absoluteFidelity is not None:
for oneFile in self.lstInput[1:]:
edPluginExecAbsoluteFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity
is not None) and (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
edPluginExecRelativeFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity
is not None) and (self.relativeFidelity is not None):
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity) and (self.dictSimilarities[
(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None):
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None):
if (self.dictSimilarities[(idx - 1, idx)] >=
self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstSummary.append("Merging files: " + " ".join(
[os.path.basename(i.path.value) for i in self.lstMerged]))
self.__edPluginExecDataver = self.loadPlugin(
self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(
self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(
self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_5.process")
xsdwf = XSDataInputWaitMultiFile(
timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist" % dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist" % inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
self.addExecutiveSummaryLine(
"Got only one frame ... nothing to merge !!!")
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity
is not None):
if self.absoluteFidelity is not None:
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[0], self.lstInput[1]])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" %
(idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity
is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity) and (self.dictSimilarities[
(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None):
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
self.resynchronize()
if (self.dictSimilarities[(idx - 1, idx)] >=
self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(
self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.addExecutiveSummaryLine("WARNING: " +
self.strRadiationDamage)
self.addExecutiveSummaryLine("Merging files: " + " ".join(
[os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value,
self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(
self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
# outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(
self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(
self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer
is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(
self.__strControlledPluginAutoSub)
base = "_".join(
os.path.basename(
self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile),
base + "_" + suff)
xsdSubtractedCurve = XSDataFile(XSDataString(sub))
self.curves.append(xsdSubtractedCurve)
self.__edPluginExecAutoSub.dataInput = XSDataInputAutoSub(
sampleCurve=self.__class__.lastSample,
buffers=[
self.__class__.lastBuffer, self.dataInput.mergedCurve
],
subtractedCurve=xsdSubtractedCurve)
self.__edPluginExecAutoSub.connectSUCCESS(
self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(
self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
if self.isFailure():
return
self.__edPluginSaxsAnalysis = self.loadPlugin(
self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(
scatterCurve=xsdSubtractedCurve,
autoRg=self.autoRg,
graphFormat=XSDataString("png"))
self.__edPluginSaxsAnalysis.connectSUCCESS(
self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(
self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
self.__class__.lastSample = None
else:
self.__class__.lastSample = self.dataInput.mergedCurve
if self.dataInput.sample and self.dataInput.sample.login and self.dataInput.sample.passwd and self.dataInput.sample.measurementID:
self.addExecutiveSummaryLine("Registering to ISPyB")
self.__edPluginSaxsISPyB = self.loadPlugin(
self.__strControlledPluginSaxsISPyB)
if len(self.lstInput) > 1:
frameAverage = XSDataInteger(len(self.lstInput))
frameMerged = XSDataInteger(len(self.lstMerged))
else:
frameMerged = frameAverage = XSDataInteger(1)
self.curves = [XSDataFile(i.path) for i in self.lstInput]
if self.strMergedFile is not None:
self.curves.append(XSDataFile(XSDataString(
self.strMergedFile)))
xsdin = XSDataInputBioSaxsISPyBv1_0(
sample=self.dataInput.sample,
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.volume,
frameAverage=frameAverage,
frameMerged=frameMerged,
curves=self.curves,
bestBuffer=self.xsBestBuffer,
scatterPlot=self.xsScatterPlot,
guinierPlot=self.xsGuinierPlot,
kratkyPlot=self.xsKratkyPlot,
densityPlot=self.xsDensityPlot
# destination=self.dataInput.sample.ispybDestination #duplicate, already in sample
)
self.__edPluginSaxsISPyB.dataInput = xsdin
self.__edPluginSaxsISPyB.connectSUCCESS(self.doSuccessISPyB)
self.__edPluginSaxsISPyB.connectFAILURE(self.doFailureISPyB)
self.__edPluginSaxsISPyB.execute()
