def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage, _xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.setImage(XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput()
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection()
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux_end()
if fFlux is not None:
self.screen("ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" % fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" % fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(xsDataSize)
# Get transmission if it's not already there
if xsDataExperimentalCondition.beam.transmission is None:
fTransmission = xsDataISPyBDataCollection.transmission
xsDataExperimentalCondition.beam.transmission = XSDataDouble(fTransmission)
if not bFoundValidFlux:
self.screen("No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data.")
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" % fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux lower than threshold flux %g photons/s!" % self.fFluxThreshold)
self.screen("Forcing flux to 0.0 photons/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
else:
# Force missing flux to 0.0
self.screen("No flux neither in ISPyB nor in mxCuBE, forcing flux to 0.0 photon/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
return xsDataExperimentalCondition
def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage,
_xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataInputRetrieveDataCollection.setImage(
XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(
xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput(
)
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection(
)
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux()
if fFlux is not None:
self.screen(
"ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(
XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" %
fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" %
fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(
xsDataSize)
if not bFoundValidFlux:
self.screen(
"No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data."
)
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" %
fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux invalid!")
return xsDataExperimentalCondition
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
self.xsDataInputCharacterisation.setToken(self.xsDataToken)
def from_params(self, data_collection, char_params):
edna_input = XSDataInputMXCuBE.parseString(self.edna_default_input)
if data_collection.id:
edna_input.setDataCollectionId(XSDataInteger(data_collection.id))
#Beam object
beam = edna_input.getExperimentalCondition().getBeam()
try:
transmission = self.collect_obj.get_transmission()
beam.setTransmission(XSDataDouble(transmission))
except AttributeError:
pass
try:
wavelength = self.collect_obj.get_wavelength()
beam.setWavelength(XSDataWavelength(wavelength))
except AttributeError:
pass
try:
beam.setFlux(XSDataFlux(self.collect_obj.get_measured_intensity()))
except AttributeError:
pass
try:
beamsize = self.get_beam_size()
if not None in beamsize:
beam.setSize(
XSDataSize(x=XSDataLength(float(beamsize[0])),
y=XSDataLength(float(beamsize[1]))))
except AttributeError:
pass
#Optimization parameters
diff_plan = edna_input.getDiffractionPlan()
aimed_i_sigma = XSDataDouble(char_params.aimed_i_sigma)
aimed_completness = XSDataDouble(char_params.aimed_completness)
aimed_multiplicity = XSDataDouble(char_params.aimed_multiplicity)
aimed_resolution = XSDataDouble(char_params.aimed_resolution)
complexity = char_params.strategy_complexity
complexity = XSDataString(qme.STRATEGY_COMPLEXITY[complexity])
permitted_phi_start = XSDataAngle(char_params.permitted_phi_start)
_range = char_params.permitted_phi_end - char_params.permitted_phi_start
rotation_range = XSDataAngle(_range)
diff_plan.setAimedIOverSigmaAtHighestResolution(aimed_i_sigma)
diff_plan.setAimedCompleteness(aimed_completness)
if char_params.use_aimed_multiplicity:
diff_plan.setAimedMultiplicity(aimed_multiplicity)
if char_params.use_aimed_resolution:
diff_plan.setAimedResolution(aimed_resolution)
diff_plan.setComplexity(complexity)
if char_params.use_permitted_rotation:
diff_plan.setUserDefinedRotationStart(permitted_phi_start)
diff_plan.setUserDefinedRotationRange(rotation_range)
#Vertical crystal dimension
sample = edna_input.getSample()
sample.getSize().setY(XSDataLength(char_params.max_crystal_vdim))
sample.getSize().setZ(XSDataLength(char_params.min_crystal_vdim))
#Radiation damage model
sample.setSusceptibility(XSDataDouble(char_params.rad_suscept))
sample.setChemicalComposition(None)
sample.setRadiationDamageModelBeta(XSDataDouble(char_params.beta /
1e6))
sample.setRadiationDamageModelGamma(
XSDataDouble(char_params.gamma / 1e6))
diff_plan.setForcedSpaceGroup(XSDataString(char_params.space_group))
# Characterisation type - Routine DC
if char_params.use_min_dose:
pass
if char_params.use_min_time:
time = XSDataTime(char_params.min_time)
diff_plan.setMaxExposureTimePerDataCollection(time)
# Account for radiation damage
if char_params.induce_burn:
diff_plan.setStrategyOption(XSDataString("-DamPar"))
else:
diff_plan.setStrategyOption(None)
# Characterisation type - SAD
if char_params.opt_sad:
diff_plan.setAnomalousData(XSDataBoolean(True))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
#Data set
data_set = XSDataMXCuBEDataSet()
acquisition_parameters = data_collection.acquisitions[
0].acquisition_parameters
path_template = data_collection.acquisitions[0].path_template
path_str = os.path.join(path_template.directory,
path_template.get_image_file_name())
for img_num in range(int(acquisition_parameters.num_images)):
image_file = XSDataFile()
path = XSDataString()
path.setValue(path_str % (img_num + 1))
image_file.setPath(path)
data_set.addImageFile(image_file)
edna_input.addDataSet(data_set)
edna_input.process_directory = path_template.process_directory
return edna_input
def testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(
pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(
pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
def testSetDataModelInput(self):
# Crystal
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataRaddoseInput = XSDataRaddoseInput()
from XSDataCommon import XSDataString
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataInteger
from XSDataRaddosev10 import XSDataCell
from XSDataRaddosev10 import XSDataAtom
from XSDataRaddosev10 import XSDataAtomicComposition
xsDataAtomSulfur = XSDataAtom()
xsDataAtomSulfur.setNumberOf(XSDataDouble(4))
xsDataAtomSulfur.setSymbol(XSDataString("S"))
xsDataAtomSelenium = XSDataAtom()
xsDataAtomSelenium.setNumberOf(XSDataDouble(4))
xsDataAtomSelenium.setSymbol(XSDataString("Se"))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtomSulfur)
xsDataAtomicComposition.addAtom(xsDataAtomSelenium)
xsDataRaddoseInput.setCrystalPATM(xsDataAtomicComposition)
xsDataRaddoseInput.setCrystalNRES(XSDataInteger(295))
xsDataRaddoseInput.setCrystalNMON(XSDataInteger(8))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataSizeCrystal = XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1))
xsDataRaddoseInput.setCrystalCell(xsDataCell)
xsDataRaddoseInput.setCrystalSize(xsDataSizeCrystal)
# Beam
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataTime
xsDataSize = XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1))
xsDataRaddoseInput.setBeamSize(xsDataSize)
xsDataRaddoseInput.setBeamFlux(XSDataFlux(1e+12))
xsDataRaddoseInput.setBeamWavelength(XSDataWavelength(2.41))
xsDataRaddoseInput.setBeamExposureTime(XSDataTime(1))
xsDataRaddoseInput.setNumberOfImages(XSDataInteger(1))
xsDataRaddoseInput.exportToFile(self.strObtainedInputFile)
strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
strObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataRaddoseInputExpected = XSDataRaddoseInput.parseString(
strExpectedInput)
xsDataRaddoseInputObtained = XSDataRaddoseInput.parseString(
strObtainedInput)
EDAssert.equal(xsDataRaddoseInputExpected.marshal(),
xsDataRaddoseInputObtained.marshal())
def testSetDataModelInput(self):
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
# Beam
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataFloat
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataExperimentalCondition
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1)))
xsBeam.setMinExposureTimePerImage(XSDataFloat(0.1))
xsExperimentalCondition.setBeam(xsBeam)
# Goniostat
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataAngle
from XSDataMXv1 import XSDataGoniostat
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setMaxOscillationSpeed(XSDataSpeed(0.2))
xsDataGoniostat.setMinOscillationWidth(XSDataAngle(0.1))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataInputCCP4i.setExperimentalCondition(xsExperimentalCondition)
# Sample
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
from XSDataCommon import XSDataString
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataFloat(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataFloat(1))
xsDataChain2.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataFloat(2))
xsDataLigand.setNumberOfLightAtoms(XSDataFloat(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataFloat(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataFloat(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataFloat(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataFloat(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.2), XSDataLength(0.2), XSDataLength(0.2)))
xsDataSampleCrystalMM.setSusceptibility(XSDataFloat(1.5))
xsDataSampleCrystalMM.setShape(XSDataFloat(2))
xsDataInputCCP4i.setSample(xsDataSampleCrystalMM)
from XSDataMXv1 import XSDataDiffractionPlan
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setAimedCompleteness(XSDataFloat(95.5))
xsDataDiffractionPlan.setAimedIOverSigmaAtHighestResolution(XSDataFloat(2.5))
xsDataDiffractionPlan.setAimedMultiplicity(XSDataFloat(95.5))
xsDataDiffractionPlan.setAimedResolution(XSDataFloat(3))
xsDataDiffractionPlan.setComplexity(XSDataString("full"))
xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString("P222"))
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataFloat(10000))
xsDataInputCCP4i.setDiffractionPlan(xsDataDiffractionPlan)
from XSDataCommon import XSDataFile
listInputDataFile = []
xsDataFile = XSDataFile(XSDataString(self.strXSDataGenerateTemplateFile))
listInputDataFile.append(xsDataFile)
xsDataInputCCP4i.setDataFile(listInputDataFile)
def testGetXSDataRaddoseInput(self):
"""
"""
from XSDataCommon import XSDataLength
from XSDataCommon import XSDataWavelength
from XSDataCommon import XSDataFlux
from XSDataCommon import XSDataSize
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataInteger
from XSDataMXv1 import XSDataBeam
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataSpaceGroup
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
from XSDataRaddosev10 import XSDataRaddoseInput
xsDataBeam = XSDataBeam()
xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1),
y=XSDataLength(0.1)))
xsDataBeam.setWavelength(XSDataWavelength(2.41))
xsDataBeam.setFlux(XSDataFlux(1e+12))
xsDataBeam.setExposureTime(XSDataTime(0.037))
xsDataSample = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("S"))
xsDataAtom2.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Fe"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomNa = XSDataAtom()
xsDataAtomNa.setSymbol(XSDataString("Na"))
xsDataAtomNa.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomNa)
xsDataAtomCl = XSDataAtom()
xsDataAtomCl.setSymbol(XSDataString("Cl"))
xsDataAtomCl.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtomCl)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSample.setChemicalComposition(xsDataComposition)
xsDataSample.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSample.setCrystal(xsDataCrystal)
iNumSymOperators = 4
iNumberOfImages = 2
xsDataRaddosev01Input = EDHandlerXSDataRaddosev10(
).getXSDataRaddoseInput(xsDataBeam, xsDataSample, iNumSymOperators,
iNumberOfImages)
xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
strExpectedInput = EDUtilsTest.readAndParseFile(
self.strReferenceInputFile2)
strObtainedInput = EDUtilsTest.readAndParseFile(
self.strObtainedInputFile2)
xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamExposureTime': obj_ = XSDataTime() obj_.build(child_) self.setBeamExposureTime(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamFlux': obj_ = XSDataFlux() obj_.build(child_) self.setBeamFlux(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamSize': obj_ = XSDataSize() obj_.build(child_) self.setBeamSize(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamWavelength': obj_ = XSDataWavelength() obj_.build(child_) self.setBeamWavelength(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalCell': obj_ = XSDataCell() obj_.build(child_) self.setCrystalCell(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalNDNA': obj_ = XSDataInteger() obj_.build(child_) self.setCrystalNDNA(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalNMON': obj_ = XSDataInteger() obj_.build(child_) self.setCrystalNMON(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalNRES': obj_ = XSDataInteger() obj_.build(child_) self.setCrystalNRES(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalNRNA': obj_ = XSDataInteger() obj_.build(child_) self.setCrystalNRNA(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalPATM': obj_ = XSDataAtomicComposition() obj_.build(child_) self.setCrystalPATM(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalSATM': obj_ = XSDataAtomicComposition() obj_.build(child_) self.setCrystalSATM(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'crystalSize': obj_ = XSDataSize() obj_.build(child_) self.setCrystalSize(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'numberOfImages': obj_ = XSDataInteger() obj_.build(child_) self.setNumberOfImages(obj_) XSDataInput.buildChildren(self, child_, nodeName_)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsdOut = _edPlugin.getDataOutput()
if xsdOut is None:
strErr = "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader: xsdataResult is None"
EDVerbose.ERROR(strErr)
self.setFailure()
raise RuntimeError(strErr)
xsDataDictionaryHeader = xsdOut.getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
