def doSuccessExecSaxsMac(self, _edPlugin=None):
self.DEBUG("EDPluginBioSaxsNormalizev1_0.doSuccessExecSaxsMac")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsNormalizev1_0.doSuccessExecSaxsMac")
strEdnaLogFile = os.path.join(self.__edPluginExecSaxsMac.getWorkingDirectory(), self.__edPluginExecSaxsMac.getScriptLogFileName())
self.DEBUG("ExecPlugin log file is in: %s" % strEdnaLogFile)
if os.path.isfile(self.strNormalizedImage) and self.isVerboseDebug():
shutil.copy(self.strNormalizedImage, self.strNormalizedImage + ".bak")
if os.path.isfile(strEdnaLogFile):
shutil.copy(strEdnaLogFile, self.strLogFile)
xsLogFile = XSDataFile()
xsLogFile.setPath(XSDataString(self.strLogFile))
self.xsdResult.setLogFile(xsLogFile)
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.xsdInput.normalizedImage)
xsdiMetadata.setOutputImage(self.xsdInput.normalizedImage)
xsdiMetadata.setBeamStopDiode(self.xsdInput.experimentSetup.beamStopDiode)
xsdiMetadata.setNormalizationFactor(self.xsdInput.experimentSetup.normalizationFactor)
xsdiMetadata.setDetector(self.xsdInput.experimentSetup.getDetector())
xsdiMetadata.setMachineCurrent(self.xsdInput.experimentSetup.machineCurrent)
xsdiMetadata.setMaskFile(self.xsdInput.experimentSetup.maskFile)
xsdiMetadata.setDetectorDistance(self.xsdInput.experimentSetup.detectorDistance)
xsdiMetadata.setWavelength(self.xsdInput.experimentSetup.wavelength)
xsdiMetadata.setPixelSize_1(self.xsdInput.experimentSetup.pixelSize_1)
xsdiMetadata.setPixelSize_2(self.xsdInput.experimentSetup.pixelSize_2)
xsdiMetadata.setBeamCenter_1(self.xsdInput.experimentSetup.beamCenter_1)
xsdiMetadata.setBeamCenter_2(self.xsdInput.experimentSetup.beamCenter_2)
xsdiMetadata.setConcentration(self.xsdInput.sample.concentration)
xsdiMetadata.setComments(self.xsdInput.sample.comments)
xsdiMetadata.setCode(self.xsdInput.sample.code)
self.__edPluginExecMetadata.setDataInput(xsdiMetadata)
def doSuccessWaitMultiFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAveragev1_0.doSuccessWaitMultiFile")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginBioSaxsAveragev1_0.doSuccessWaitMultiFile")
self.strProcessLog += "Retrieve metadata from file %s\n" % (
self.integratedImages[0])
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.getIntegratedImage()[0])
xsdiMetadata.setConcentration(self.dataInput.concentration)
xsdiMetadata.setComments(self.dataInput.comments)
xsdiMetadata.setCode(self.dataInput.code)
xsdiMetadata.setDetector(self.dataInput.getDetector())
xsdiMetadata.setDetectorDistance(self.dataInput.detectorDistance)
xsdiMetadata.setPixelSize_1(self.dataInput.pixelSize_1)
xsdiMetadata.setPixelSize_2(self.dataInput.pixelSize_2)
xsdiMetadata.setBeamCenter_1(self.dataInput.beamCenter_1)
xsdiMetadata.setBeamCenter_2(self.dataInput.beamCenter_2)
xsdiMetadata.setWavelength(self.dataInput.wavelength)
xsdiMetadata.setMachineCurrent(self.dataInput.machineCurrent)
xsdiMetadata.setMaskFile(self.dataInput.maskFile)
xsdiMetadata.setNormalizationFactor(self.dataInput.normalizationFactor)
self.__edPluginSaxsGetMetadata.setDataInput(xsdiMetadata)
self.__edPluginSaxsGetMetadata.connectSUCCESS(self.doSucessGetMetadata)
self.__edPluginSaxsGetMetadata.connectFAILURE(
self.doFailureGetMetadata)
self.__edPluginSaxsGetMetadata.executeSynchronous()
def doSuccessWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAsciiExportv1_0.doSuccessWaitFile")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginBioSaxsAsciiExportv1_0.doSuccessWaitFile")
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.getIntegratedImage())
self.__edPluginSaxsGetMetadata.setDataInput(xsdiMetadata)
def testCheckParameters(self):
xsDataInput = XSDataInputBioSaxsMetadatav1_0()
xsDataInput.setInputImage(XSDataImage())
EDVerbose.DEBUG("xsdIn:%s" % xsDataInput.marshal())
edPluginExec = self.createPlugin()
edPluginExec.setDataInput(xsDataInput)
edPluginExec.checkParameters()
def doSuccessWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAzimutIntv1_0.doSuccessWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsAzimutIntv1_0.doSuccessWaitFile")
self.strProcessLog += "Retrieve metadata from file %s\n" % (self.normalizedImage)
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.normalizedImage)
xsdiMetadata.setConcentration(self.sample.concentration)
xsdiMetadata.setComments(self.sample.comments)
xsdiMetadata.setCode(self.sample.code)
xsdiMetadata.setDetector(self.exprimentSetup.getDetector())
xsdiMetadata.setDetectorDistance(self.exprimentSetup.detectorDistance)
xsdiMetadata.setPixelSize_1(self.exprimentSetup.pixelSize_1)
xsdiMetadata.setPixelSize_2(self.exprimentSetup.pixelSize_2)
xsdiMetadata.setBeamCenter_1(self.exprimentSetup.beamCenter_1)
xsdiMetadata.setBeamCenter_2(self.exprimentSetup.beamCenter_2)
xsdiMetadata.setWavelength(self.exprimentSetup.wavelength)
xsdiMetadata.setMachineCurrent(self.exprimentSetup.machineCurrent)
xsdiMetadata.setMaskFile(self.exprimentSetup.maskFile)
xsdiMetadata.setNormalizationFactor(self.exprimentSetup.normalizationFactor)
self.__edPluginSaxsGetMetadata.setDataInput(xsdiMetadata)
def doSuccessWaitFile(self, _edPlugin=None):
self.DEBUG("EDPluginBioSaxsAzimutIntv1_3.doSuccessWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsAzimutIntv1_3.doSuccessWaitFile")
self.lstProcessLog.append("Retrieve metadata from file %s" % (self.normalizedImage))
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.inputImage = self.dataInput.normalizedImage
xsdiMetadata.concentration = self.sample.concentration
xsdiMetadata.comments = self.sample.comments
xsdiMetadata.code = self.sample.code
xsdiMetadata.detector = self.experimentSetup.detector
xsdiMetadata.detectorDistance = self.experimentSetup.detectorDistance
xsdiMetadata.pixelSize_1 = self.experimentSetup.pixelSize_1
xsdiMetadata.pixelSize_2 = self.experimentSetup.pixelSize_2
xsdiMetadata.beamCenter_1 = self.experimentSetup.beamCenter_1
xsdiMetadata.beamCenter_2 = self.experimentSetup.beamCenter_2
xsdiMetadata.wavelength = self.experimentSetup.wavelength
xsdiMetadata.machineCurrent = self.experimentSetup.machineCurrent
xsdiMetadata.maskFile = self.experimentSetup.maskFile
xsdiMetadata.normalizationFactor = self.experimentSetup.normalizationFactor
xsdiMetadata.beamStopDiode = self.experimentSetup.beamStopDiode
self.__edPluginMetadata.dataInput = xsdiMetadata
def doSuccessSaxsAdd(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAzimutIntv1_0.doSuccessSaxsAdd")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsAzimutIntv1_0.doSuccessSaxsAdd")
self.xsdResult.setCorrectedImage(self.dataInput.getCorrectedImage())
self.strProcessLog += "Appending metadata to Corrected EDF image '%s'.\n" % (self.correctedImage)
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.getCorrectedImage())
xsdiMetadata.setOutputImage(self.dataInput.getCorrectedImage())
xsdiMetadata.setConcentration(self.xsdMetadata.concentration)
xsdiMetadata.setComments(self.xsdMetadata.comments)
xsdiMetadata.setCode(self.xsdMetadata.code)
xsdiMetadata.setDetector(self.xsdMetadata.getDetector())
xsdiMetadata.setDetectorDistance(self.xsdMetadata.detectorDistance)
xsdiMetadata.setPixelSize_1(self.xsdMetadata.pixelSize_1)
xsdiMetadata.setPixelSize_2(self.xsdMetadata.pixelSize_2)
xsdiMetadata.setBeamCenter_1(self.xsdMetadata.beamCenter_1)
xsdiMetadata.setBeamCenter_2(self.xsdMetadata.beamCenter_2)
xsdiMetadata.setWavelength(self.xsdMetadata.wavelength)
xsdiMetadata.setMachineCurrent(self.xsdMetadata.machineCurrent)
xsdiMetadata.setMaskFile(self.xsdMetadata.maskFile)
xsdiMetadata.setNormalizationFactor(self.xsdMetadata.normalizationFactor)
self.__edPluginSaxsSetMetadata.setDataInput(xsdiMetadata)
def doSuccessWaitFile(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAsciiExportv1_1.doSuccessWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginBioSaxsAsciiExportv1_1.doSuccessWaitFile")
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.getIntegratedImage())
if self.dataInput.sample is not None:
xsdiMetadata.code = self.dataInput.sample.code
xsdiMetadata.concentration = self.dataInput.sample.concentration
xsdiMetadata.comments = self.dataInput.sample.comments
if self.dataInput.experimentSetup is not None:
xsdiMetadata.detector = self.dataInput.experimentSetup.detector
xsdiMetadata.detectorDistance = self.dataInput.experimentSetup.detectorDistance
# this is deliberately taken out as pixels size are redefined during integration JK
# xsdiMetadata.pixelSize_1 = self.dataInput.experimentSetup.pixelSize_1
# xsdiMetadata.pixelSize_2 = self.dataInput.experimentSetup.pixelSize_2
xsdiMetadata.beamCenter_1 = self.dataInput.experimentSetup.beamCenter_1
xsdiMetadata.beamCenter_2 = self.dataInput.experimentSetup.beamCenter_2
xsdiMetadata.beamStopDiode = self.dataInput.experimentSetup.beamStopDiode
xsdiMetadata.wavelength = self.dataInput.experimentSetup.wavelength
xsdiMetadata.machineCurrent = self.dataInput.experimentSetup.machineCurrent
xsdiMetadata.maskFile = self.dataInput.experimentSetup.maskFile
xsdiMetadata.normalizationFactor = self.dataInput.experimentSetup.normalizationFactor
self.__edPluginSaxsGetMetadata.setDataInput(xsdiMetadata)
def doSuccessSaxsMac(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginBioSaxsAveragev1_0.doSuccessSaxsMac")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginBioSaxsAveragev1_0.doSuccessSaxsMac")
strEdnaLogFile = os.path.join(_edPlugin.getWorkingDirectory(),
_edPlugin.getScriptLogFileName())
EDVerbose.DEBUG("ExecPlugin log file is in: %s" % strEdnaLogFile)
if os.path.isfile(strEdnaLogFile):
shutil.copy(strEdnaLogFile, self.strLogFile)
xsLogFile = XSDataFile()
xsLogFile.setPath(XSDataString(self.strLogFile))
self.xsdResult.setLogFile(xsLogFile)
xsdiMetadata = XSDataInputBioSaxsMetadatav1_0()
xsdiMetadata.setInputImage(self.dataInput.getAveragedImage())
xsdiMetadata.setOutputImage(self.dataInput.getAveragedImage())
xsdiMetadata.setConcentration(self.xsdMetadata.concentration)
xsdiMetadata.setComments(self.xsdMetadata.comments)
xsdiMetadata.setCode(self.xsdMetadata.code)
xsdiMetadata.setDetector(self.xsdMetadata.getDetector())
xsdiMetadata.setDetectorDistance(self.xsdMetadata.detectorDistance)
xsdiMetadata.setPixelSize_1(self.xsdMetadata.pixelSize_1)
xsdiMetadata.setPixelSize_2(self.xsdMetadata.pixelSize_2)
xsdiMetadata.setBeamCenter_1(self.xsdMetadata.beamCenter_1)
xsdiMetadata.setBeamCenter_2(self.xsdMetadata.beamCenter_2)
xsdiMetadata.setWavelength(self.xsdMetadata.wavelength)
xsdiMetadata.setMachineCurrent(self.xsdMetadata.machineCurrent)
xsdiMetadata.setMaskFile(self.xsdMetadata.maskFile)
xsdiMetadata.setNormalizationFactor(
self.xsdMetadata.normalizationFactor)
self.__edPluginSaxsSetMetadata.setDataInput(xsdiMetadata)
self.__edPluginSaxsSetMetadata.connectSUCCESS(
self.doSuccessSetMetadata)
self.__edPluginSaxsSetMetadata.connectFAILURE(
self.doFailureSetMetadata)
self.__edPluginSaxsSetMetadata.executeSynchronous()