def generateDataMOSFLMInputGeneratePrediction(self):
"""
"""
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(102.5))
xsDataMOSFLMBeamPosition.setY(XSDataLength(104.7))
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
from XSDataMOSFLMv10 import XSDataMOSFLMImage
xsDataMOSFLMImage1 = XSDataMOSFLMImage()
xsDataMOSFLMImage1.setNumber(XSDataInteger(1))
xsDataMOSFLMImage1.setRotationAxisStart(XSDataAngle(0.0))
xsDataMOSFLMImage1.setRotationAxisEnd(XSDataAngle(1.0))
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction(
)
xsDataMOSFLMInputGeneratePrediction.setDistance(XSDataLength(198.4))
xsDataMOSFLMInputGeneratePrediction.setWavelength(
XSDataWavelength(0.9340))
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputGeneratePrediction.setDirectory(
XSDataString(self.strDataImagePath))
xsDataMOSFLMInputGeneratePrediction.setTemplate(
XSDataString("ref-testscale_1_###.img"))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage1)
return xsDataMOSFLMInputGeneratePrediction
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'symmetry':
obj_ = XSDataString()
obj_.build(child_)
self.setSymmetry(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'orientation':
obj_ = XSDataXOalignOrientation()
obj_.build(child_)
self.setOrientation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'cell':
obj_ = XSDataXOalignCell()
obj_.build(child_)
self.setCell(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'omega':
obj_ = XSDataAngle()
obj_.build(child_)
self.setOmega(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'kappa':
obj_ = XSDataAngle()
obj_.build(child_)
self.setKappa(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'phi':
obj_ = XSDataAngle()
obj_.build(child_)
self.setPhi(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataLength
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataCell
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataLength(78.9),
XSDataLength(95.162),
XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
strChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", strChainType.getValue())
def collectionRunItemListToCollectionRun(self, _xsCollectionRunItemList):
xsDataCollectionRun = XSDataBestCollectionRun()
xsItemExposureTime = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "exposure_time")
fExposureTime = float(xsItemExposureTime.getValueOf_())
xsDataCollectionRun.setExposureTime(XSDataTime(fExposureTime))
xsItemDistance = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"distance")
fDistance = float(xsItemDistance.getValueOf_())
xsDataCollectionRun.setDistance(XSDataLength(fDistance))
xsItemRotationAxisStart = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "phi_start")
fRotationAxisStart = float(xsItemRotationAxisStart.getValueOf_())
xsDataCollectionRun.setPhiStart(XSDataAngle(fRotationAxisStart))
xsNumberOfImages = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "number_of_images")
iNumberOfImages = int(xsNumberOfImages.getValueOf_())
xsDataCollectionRun.setNumberOfImages(XSDataInteger(iNumberOfImages))
xsItemPhiWidth = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"phi_width")
fPhiWidth = float(xsItemPhiWidth.getValueOf_())
xsDataCollectionRun.setPhiWidth(XSDataAngle(fPhiWidth))
xsItemOverlaps = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"overlaps")
strOverlaps = xsItemOverlaps.getValueOf_()
xsDataCollectionRun.setOverlaps(XSDataString(strOverlaps))
return xsDataCollectionRun
def populateXSDataInputSPDCake(dictID11):
xsDataInputSPDCake = XSDataInputSPDCake()
# Angle of tilt
xsDataInputSPDCake.setAngleOfTilt(
XSDataAngle(float(dictID11["ANGLE OF TILT"])))
# Dark current
if dictID11["DARK CURRENT"] == "YES":
xsDataInputSPDCake.setDarkCurrentImageFile(
XSDataFile(XSDataString(dictID11["DC FILE"])))
#xsDataFile = XSDataFile()
#xsDataFile.setPath(XSDataString(dictID11["DC FILE "]))
#xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
if dictID11["FLAT-FIELD"] == "YES":
xsDataInputSPDCake.setFlatFieldImageFile(
XSDataFile(XSDataString(dictID11["FF FILE"])))
if dictID11["FF SCALE"] == "NO":
xsDataInputSPDCake.setFlatFieldImageFile(
XSDataFile(XSDataString(dictID11["FF MULTIPLIER"])))
if dictID11["SPATIAL DIS."] == "YES":
xsDataInputSPDCake.setSpatialDistortionFile(
XSDataFile(XSDataString(dictID11["SD FILE"])))
xsDataInputSPDCake.setStartAzimuth(
XSDataAngle(float(dictID11["START AZIMUTH"])))
xsDataInputSPDCake.setStopAzimuth(
XSDataAngle(float(dictID11["END AZIMUTH"])))
xsDataInputSPDCake.setInnerRadius(
XSDataDouble(float(dictID11["INNER RADIUS"])))
xsDataInputSPDCake.setOuterRadius(
XSDataDouble(float(dictID11["OUTER RADIUS"])))
xsDataInputSPDCake.setBufferSizeX(
XSDataInteger(int(dictID11["X-PIXEL SIZE"])))
xsDataInputSPDCake.setBufferSizeY(
XSDataInteger(int(dictID11["Y-PIXEL SIZE"])))
xsDataInputSPDCake.setSampleToDetectorDistance(
XSDataLength(float(dictID11["DISTANCE"])))
xsDataInputSPDCake.setWavelength(
XSDataLength(float(dictID11["WAVELENGTH"])))
xsDataInputSPDCake.setBeamCentreInPixelsX(
XSDataDouble(float(dictID11["X-BEAM CENTRE"])))
xsDataInputSPDCake.setBeamCentreInPixelsY(
XSDataDouble(float(dictID11["Y-BEAM CENTRE"])))
xsDataInputSPDCake.setTiltRotation(
XSDataAngle(float(dictID11["TILT ROTATION"])))
xsDataInputSPDCake.setOutputFileType(
XSDataFile(XSDataString(dictID11["saving_format"])))
xsDataInputSPDCake.setOutputFileType(
XSDataFile(XSDataString(dictID11["output_dir"])))
# TODO : some parameters remain not inserted in this file because not in the datamodel
print xsDataInputSPDCake.marshal()
def preProcess(self, _edObject=None):
"""
The pre-process of ED Plugin Control DiffractionCT Powder Integration consists in preparing the input data for SPD Cake.
and declares the execution plugin as EDPluginFit2DCacke
"""
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlDCTPowderIntegrationv1_1.preProcess")
# Load the execution plugin
self.m_edPluginPowderIntegration = self.loadPlugin(self.m_edStringControlledPluginName)
#Retrive its'datamodel
xsDataInputSPDCake = XSDataInputSPDCake()
instrumentParameters = self.getDataInput().getInstrumentParameters()
imageParameters = self.getDataInput().getImageParameters()
xsDataInputSPDCake.setInputFile(self.getDataInput().getImageFile())
xsDataInputSPDCake.setWavelength(instrumentParameters.get_diffrn_radiation_wavelength())
xsDataInputSPDCake.setSampleToDetectorDistance(instrumentParameters.get_pd_instr_dist_spec_detc())
xsDataInputSPDCake.setAngleOfTilt(imageParameters.get_pd_instr_special_details_tilt_angle())
xsDataInputSPDCake.setTiltRotation(imageParameters.get_pd_instr_special_details_tilt_rotation())
xsDataInputSPDCake.setDarkCurrentImageFile(imageParameters.get_file_correction_image_dark_current())
xsDataInputSPDCake.setFlatFieldImageFile(imageParameters.get_file_correction_image_flat_field())
xsDataInputSPDCake.setSpatialDistortionFile(imageParameters.get_file_correction_spline_spatial_distortion())
# EDVerbose.screen("imageParameters.get_array_element_size_1: %s" % imageParameters.get_array_element_size_1().marshal())
xsDataInputSPDCake.setBeamCentreInPixelsX(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_1()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_1())))
xsDataInputSPDCake.setBeamCentreInPixelsY(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_2()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_2())))
xsDataInputSPDCake.setPixelSizeX(imageParameters.get_array_element_size_1())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setPixelSizeY(imageParameters.get_array_element_size_2())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setBufferSizeX(XSDataInteger(2048))
xsDataInputSPDCake.setBufferSizeY(XSDataInteger(2048))
xsDataInputSPDCake.setStartAzimuth(XSDataAngle(0))
xsDataInputSPDCake.setStopAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setStepAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setOutputDirCake(self.getDataInput().getDestinationDir())
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(True))
try:
self.m_edPluginPowderIntegration.setDataInput(xsDataInputSPDCake)
except Exception, error:
# This exception handling needs to be rethought, see bug #43.
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlDCTPowderIntegrationv1_1.preProcess: Unexpected error in SPD handler: ", error)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def collectionRunItemListToCollectionRun(self, _xsCollectionRunItemList,
_iCollectionRunNumber):
xsDataCollectionRun = XSDataBestCollectionRun()
xsItemWedge = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"Wedge")
if xsItemWedge is not None:
iWedge = int(xsItemWedge.getValueOf_())
else:
iWedge = _iCollectionRunNumber
xsDataCollectionRun.setCollectionRunNumber(XSDataInteger(iWedge))
xsItemCrystal = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"Crystal")
if xsItemCrystal is not None:
iCrystal = int(xsItemCrystal.getValueOf_())
xsDataCollectionRun.setCrystalPosition(XSDataInteger(iCrystal))
xsItemExposureTime = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "exposure_time")
fExposureTime = float(xsItemExposureTime.getValueOf_())
xsDataCollectionRun.setExposureTime(XSDataTime(fExposureTime))
xsItemAction = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"action")
if (xsItemAction is not None):
strAction = xsItemAction.getValueOf_()
xsDataCollectionRun.setAction(XSDataString(strAction))
xsItemRotationAxisStart = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "phi_start")
fRotationAxisStart = float(xsItemRotationAxisStart.getValueOf_())
xsDataCollectionRun.setPhiStart(XSDataAngle(fRotationAxisStart))
xsNumberOfImages = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "number_of_images")
iNumberOfImages = int(xsNumberOfImages.getValueOf_())
xsDataCollectionRun.setNumberOfImages(XSDataInteger(iNumberOfImages))
xsItemPhiWidth = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"phi_width")
fPhiWidth = float(xsItemPhiWidth.getValueOf_())
xsDataCollectionRun.setPhiWidth(XSDataAngle(fPhiWidth))
xsItemOverlaps = EDUtilsTable.getItemFromList(_xsCollectionRunItemList,
"overlaps")
if (xsItemOverlaps is not None):
strOverlaps = xsItemOverlaps.getValueOf_()
xsDataCollectionRun.setOverlaps(XSDataString(strOverlaps))
xsItemTransmission = EDUtilsTable.getItemFromList(
_xsCollectionRunItemList, "transmission")
if (xsItemTransmission is not None):
fTransmission = float(xsItemTransmission.getValueOf_())
xsDataCollectionRun.setTransmission(XSDataDouble(fTransmission))
return xsDataCollectionRun
def readIdxrefLp(self, _pathToIdxrefLp, _xsDataResultXDSIndexing=None):
self.DEBUG("EDPluginXDSIndexingv1_0.readIdxrefLp")
if _xsDataResultXDSIndexing is None:
xsDataResultXDSIndexing = XSDataResultXDSIndexing()
else:
xsDataResultXDSIndexing = _xsDataResultXDSIndexing
if os.path.exists(_pathToIdxrefLp):
xsDataResultXDSIndexing.pathToLogFile = XSDataFile(XSDataString(_pathToIdxrefLp))
with open(_pathToIdxrefLp) as f:
listLines = f.readlines()
indexLine = 0
doParseParameters = False
doParseLattice = False
while (indexLine < len(listLines)):
if "DIFFRACTION PARAMETERS USED AT START OF INTEGRATION" in listLines[indexLine]:
doParseParameters = True
doParseLattice = False
elif "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE" in listLines[indexLine]:
doParseParameters = False
doParseLattice = True
if doParseParameters:
if "MOSAICITY" in listLines[indexLine]:
mosaicity = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.mosaicity = XSDataAngle(mosaicity)
elif "DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM" in listLines[indexLine]:
xBeam = float(listLines[indexLine].split()[-2])
yBeam = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.beamCentreX = XSDataFloat(xBeam)
xsDataResultXDSIndexing.beamCentreY = XSDataFloat(yBeam)
elif "CRYSTAL TO DETECTOR DISTANCE" in listLines[indexLine]:
distance = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.distance = XSDataLength(distance)
elif doParseLattice:
if listLines[indexLine].startswith(" * ") and not listLines[indexLine + 1].startswith(" * "):
listLine = listLines[indexLine].split()
xsDataResultXDSIndexing.latticeCharacter = XSDataInteger(int(listLine[1]))
bravaisLattice = listLine[2]
xsDataResultXDSIndexing.bravaisLattice = XSDataString(bravaisLattice)
spaceGroup = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(bravaisLattice)
xsDataResultXDSIndexing.spaceGroup = XSDataString(spaceGroup)
spaceGroupNumber = EDUtilsSymmetry.getITNumberFromSpaceGroupName(spaceGroup)
xsDataResultXDSIndexing.spaceGroupNumber = XSDataInteger(spaceGroupNumber)
xsDataResultXDSIndexing.qualityOfFit = XSDataFloat(float(listLine[3]))
xsDataXDSCell = XSDataXDSCell()
xsDataXDSCell.length_a = XSDataLength(float(listLine[4]))
xsDataXDSCell.length_b = XSDataLength(float(listLine[5]))
xsDataXDSCell.length_c = XSDataLength(float(listLine[6]))
xsDataXDSCell.angle_alpha = XSDataAngle(float(listLine[7]))
xsDataXDSCell.angle_beta = XSDataAngle(float(listLine[8]))
xsDataXDSCell.angle_gamma = XSDataAngle(float(listLine[9]))
xsDataResultXDSIndexing.unitCell = xsDataXDSCell
indexLine += 1
return xsDataResultXDSIndexing
def parsePointlessOutput(self, _outputFile):
sgre = re.compile(
""" \* Space group = '(?P<sgstr>.*)' \(number\s+(?P<sgnumber>\d+)\)"""
)
sgnumber = sgstr = None
res = XSDataPointlessOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(False)
if os.path.exists(_outputFile):
res.status = status
strLog = EDUtilsFile.readFile(_outputFile)
if strLog is not None:
# we'll apply the regexp to the whole file contents which
# hopefully won't be that long.
m = sgre.search(strLog)
if m is not None:
d = m.groupdict()
sgnumber = d['sgnumber']
sgstr = d['sgstr']
res.sgnumber = XSDataInteger(sgnumber)
res.sgstr = XSDataString(sgstr)
status.isSuccess = XSDataBoolean(True)
# Search first for unit cell after the Laue group...
unitCellRe = re.compile(
""" Laue group confidence.+\\n\\n\s+Unit cell:(.+)""")
m2 = unitCellRe.search(strLog)
if m2 is None:
# Then search it from the end...
unitCellRe = re.compile(
""" \* Cell Dimensions : \(obsolete \- refer to dataset cell dimensions above\)\\n\\n(.+)"""
)
m2 = unitCellRe.search(strLog)
if m2 is not None:
listCell = m2.groups()[0].split()
xsDataCCP4Cell = XSDataCCP4Cell()
xsDataCCP4Cell.length_a = XSDataLength(listCell[0])
xsDataCCP4Cell.length_b = XSDataLength(listCell[1])
xsDataCCP4Cell.length_c = XSDataLength(listCell[2])
xsDataCCP4Cell.angle_alpha = XSDataAngle(listCell[3])
xsDataCCP4Cell.angle_beta = XSDataAngle(listCell[4])
xsDataCCP4Cell.angle_gamma = XSDataAngle(listCell[5])
res.cell = xsDataCCP4Cell
return res
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamCentreX': obj_ = XSDataLength() obj_.build(child_) self.setBeamCentreX(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'beamCentreY': obj_ = XSDataLength() obj_.build(child_) self.setBeamCentreY(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'distance': obj_ = XSDataLength() obj_.build(child_) self.setDistance(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'mosaicity': obj_ = XSDataAngle() obj_.build(child_) self.setMosaicity(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'selectedSolutionNumber': obj_ = XSDataInteger() obj_.build(child_) self.setSelectedSolutionNumber(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'labelitScreenSolution': obj_ = XSDataLabelitScreenSolution() obj_.build(child_) self.labelitScreenSolution.append(obj_) XSData.buildChildren(self, child_, nodeName_)
def mergeTwoSubWedgesAdjascentInRotationAxis(self, _subWedge1, _subWedge2):
"""
This method takes as input two sub wedges and merges them to an unique subwedge, if possible,
and returns the resulting merged sub wedge. If the merge is not possible a None is returned.
"""
EDVerbose.DEBUG(
"EDPluginSubWedgeMergev1_1.mergeTwoSubWedgesAdjascentInRotationAxis"
)
xsDataSubWedgeMerged = None
# First check that the two sub wedges have identical experimental conditions
if (self.isSameExperimentalConditionInSubWedge(_subWedge1,
_subWedge2)):
# Check if sub wedges are adjascent:
dRoationAxisEnd1 = _subWedge1.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd().getValue()
dRoationAxisStart2 = _subWedge2.getExperimentalCondition(
).getGoniostat().getRotationAxisStart().getValue()
#print dRoationAxisEnd1, dRoationAxisStart2
if (self.compareTwoValues(dRoationAxisEnd1, dRoationAxisStart2,
0.001)):
# Same sub wedge! Let's merge them
xsDataSubWedgeMerged = XSDataSubWedge.parseString(
_subWedge1.marshal())
xsDataSubWedge2 = XSDataSubWedge.parseString(
_subWedge2.marshal())
dRoationAxisEnd2 = xsDataSubWedge2.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd().getValue()
xsDataSubWedgeMerged.getExperimentalCondition().getGoniostat(
).setRotationAxisEnd(XSDataAngle(dRoationAxisEnd2))
for xsDataImage in xsDataSubWedge2.getImage():
xsDataSubWedgeMerged.addImage(xsDataImage)
return xsDataSubWedgeMerged
def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
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)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
pyStrChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", pyStrChainType.getValue())
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1InputCharacterisation':
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setMxv1InputCharacterisation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv1ResultCharacterisation_Reference':
obj_ = XSDataResultCharacterisation()
obj_.build(child_)
self.setMxv1ResultCharacterisation_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mxv2DataCollection_Reference':
obj_ = XSDataCollection()
obj_.build(child_)
self.setMxv2DataCollection_Reference(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'possibleOrientations':
obj_ = kappa_alignment_response()
obj_.build(child_)
self.setPossibleOrientations(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'omega':
obj_ = XSDataAngle()
obj_.build(child_)
self.setOmega(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'kappa':
obj_ = XSDataAngle()
obj_.build(child_)
self.setKappa(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'phi':
obj_ = XSDataAngle()
obj_.build(child_)
self.setPhi(obj_)
XSDataInputInterface.buildChildren(self, child_, nodeName_)
def unitTestGetSIValue(self):
"""
test the execution of unitTestGetSIValue static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetSIValue")
xsd = XSDataLength(1.5)
xsd.setUnit(XSDataString("mm"))
EDAssert.equal(0.0015, EDUtilsUnit.getSIValue(xsd),
"Conversion mm to meter")
xsd = XSDataAngle(90)
xsd.setUnit(XSDataString("deg"))
EDAssert.equal(math.pi / 2, EDUtilsUnit.getSIValue(xsd),
"Conversion deg to rad")
def getXSDataStrategyResult(self, _xsDataBestOutput, _xsDataExperimentalCondition, _xsDataSample):
xsDataStrategyResult = XSDataStrategyResult()
#xsDataCollectionRunsBest = _xsDataBestOutput.getCollectionRun()
xsDataCollectionPlansBest = _xsDataBestOutput.getCollectionPlan()
for xsDataCollectionPlanBest in xsDataCollectionPlansBest:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
for xsDataCollectionRunBest in xsDataCollectionPlanBest.getCollectionRun():
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(xsDataCollectionRunBest.getExposureTime())
xsDataExperimentalCondition.getDetector().setDistance(xsDataCollectionRunBest.getDistance())
xsDataExperimentalCondition.getGoniostat().setRotationAxisStart(xsDataCollectionRunBest.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(xsDataCollectionRunBest.getPhiWidth())
fRotationAxisEnd = xsDataCollectionRunBest.getPhiStart().getValue() + xsDataCollectionRunBest.getNumberOfImages().getValue() * xsDataCollectionRunBest.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(xsDataCollectionStrategy)
xsDataStrategySummary = xsDataCollectionPlanBest.getStrategySummary()
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
xsDataStatistics = xsDataCollectionPlanBest.getStatisticalPrediction()
xsDataCollectionPlan.setStatistics(xsDataStatistics)
xsDataStrategyResult.addCollectionPlan(xsDataCollectionPlan)
return xsDataStrategyResult
def getReferenceDataMOSFLMNewmat(self):
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
XSDataMatrixDoubleA = XSDataMatrixDouble()
XSDataMatrixDoubleA.setM11(-0.00826416)
XSDataMatrixDoubleA.setM12(0.00885073)
XSDataMatrixDoubleA.setM13(0.00937013)
XSDataMatrixDoubleA.setM21(0.00126554)
XSDataMatrixDoubleA.setM22(0.01251971)
XSDataMatrixDoubleA.setM23(-0.00845341)
XSDataMatrixDoubleA.setM31(-0.01484956)
XSDataMatrixDoubleA.setM32(-0.00385867)
XSDataMatrixDoubleA.setM33(-0.00593515)
xsDataMOSFLMNewmat.setAMatrix(XSDataMatrixDoubleA)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(1.000))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(2.000))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(3.000))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
XSDataMatrixDoubleU = XSDataMatrixDouble()
XSDataMatrixDoubleU.setM11(-0.4849475)
XSDataMatrixDoubleU.setM12(0.5598049)
XSDataMatrixDoubleU.setM13(0.6718960)
XSDataMatrixDoubleU.setM21(0.0742629)
XSDataMatrixDoubleU.setM22(0.7918670)
XSDataMatrixDoubleU.setM23(-0.6061614)
XSDataMatrixDoubleU.setM31(-0.8713845)
XSDataMatrixDoubleU.setM32(-0.2440595)
XSDataMatrixDoubleU.setM33(-0.4255866)
xsDataMOSFLMNewmat.setUMatrix(XSDataMatrixDoubleU)
xsDataCellRefined = XSDataCell()
xsDataCellRefined.setLength_a(XSDataLength(54.8079))
xsDataCellRefined.setLength_b(XSDataLength(59.0751))
xsDataCellRefined.setLength_c(XSDataLength(66.9736))
xsDataCellRefined.setAngle_alpha(XSDataAngle(91.0000))
xsDataCellRefined.setAngle_beta(XSDataAngle(92.0000))
xsDataCellRefined.setAngle_gamma(XSDataAngle(93.0000))
xsDataMOSFLMNewmat.setRefinedCell(xsDataCellRefined)
return xsDataMOSFLMNewmat
def setup(self, _listInput=[], _mode="offline"):
"""Configure the various options"""
bOK = False
if _listInput == []:
_listInput = [os.getcwd()]
while not bOK:
strtmp = raw_input(
"What are the input directories (mandatory, space separated) %s: "
% _listInput).strip()
if len(strtmp) > 0:
bAllExists = True
lstTemp = shlex.split(strtmp)
for oneDir in shlex.split(strtmp):
if not os.path.exists(oneDir):
EDVerbose.screen("No such file or directory: %s" %
oneDir)
bAllExists = False
if bAllExists is True:
self.listInput = lstTemp
bOK = True
else:
self.listInput = _listInput
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is operation mode [offline|online|all] (mandatory: %s): "
% _mode).strip().lower()
if len(strtmp) > 0:
bOK = True
if strtmp == "offline":
self.bNewerOnly = False
self.strMode = "OffLine"
elif strtmp == "online":
self.bNewerOnly = True
self.strMode = "dirwatch"
elif strtmp == "all":
self.bNewerOnly = False
self.strMode = "dirwatch"
else:
bOK = False
bOK = False
while not bOK:
strtmp = raw_input(
"What is the destination directory (mandatory): ").strip()
if os.path.isdir(strtmp):
self.destinationDirectory = XSDataFile()
self.destinationDirectory.setPath(
XSDataString(os.path.abspath(strtmp)))
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the sinogram filename prefix (mandatory): ").strip()
if strtmp != "":
self.sinogramFileNamePrefix = XSDataString(strtmp)
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the powder diffraction subdirectory (mandatory): "
).strip()
if strtmp != "":
self.powderDiffractionSubdirectory = XSDataString(strtmp)
bOK = True
strtmp = raw_input(
"What is the powder diffraction output format (CHI or CIF, if any ): "
).strip().lower()
if strtmp.find("cif") >= 0:
self.powderDiffractionFormat = XSDataString("cif")
elif strtmp.find("chi") >= 0:
self.powderDiffractionFormat = XSDataString("chi")
strtmp = raw_input("Process all files ending with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExtensions.append(oneExt)
strtmp = raw_input("Exclude all files starting with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExcludedPrefix.append(oneExt)
strtmp = raw_input(
"Do you want to over-ride metadata from the headers [y|N]: "
).strip().lower()
if len(strtmp) > 0 and strtmp[0] == "y":
strtmp = raw_input("What is the flat field image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
flatFieldImage = XSDataFile()
flatFieldImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_flat_field(
flatFieldImage)
strtmp = raw_input("What is the dark current image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
darkCurrentImage = XSDataFile()
darkCurrentImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_dark_current(
darkCurrentImage)
strtmp = raw_input("What is the mask file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
maskFile = XSDataFile()
maskFile.setPath(XSDataString(strtmp))
self.forceImage.set_file_correction_image_mask(maskFile)
strtmp = raw_input("What is the spline file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
splineFile = XSDataFile()
splineFile.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_spline_spatial_distortion(
splineFile)
strtmp = raw_input(
"What is the wavelength (like 0.7 A): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
wavelength = XSDataWavelength()
wavelength.setValue(f)
if len(w) == 2:
wavelength.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_diffrn_radiation_wavelength(
wavelength)
strtmp = raw_input(
"What is the distance between the sample and the detector along the beam: "
).replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
distance = XSDataLength()
distance.setValue(f)
if len(w) == 2:
distance.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_pd_instr_dist_spec_detc(distance)
strtmp = raw_input(
"What is the pixel size (like 52.8 um 53.2 um): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_array_element_size_1(xsdata1)
self.forceImage.set_array_element_size_2(xsdata2)
strtmp = raw_input(
"What is the beam center in distance, not pixels (like 53.5 mm 48.2 mm): "
).strip().replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError, IndexError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_diffrn_detector_element_center_1(
xsdata1)
self.forceImage.set_diffrn_detector_element_center_2(
xsdata2)
strtmp = raw_input("What is the detector tilt angle: ").strip()
tiltAngle = None
try:
tiltAngle = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_angle(
tiltAngle)
strtmp = raw_input("What is the tilt plan rotation: ").strip()
tiltRotation = None
try:
tiltRotation = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_rotation(
tiltRotation)
strtmp = raw_input(
"What is the number of fast motor steps (you will have n+1 points): "
).strip()
try:
self.fastMotorSteps = int(strtmp)
except ValueError:
fastMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_spec_displ_x_max(
XSDataLength(self.fastMotorSteps))
self.forceInstrument.set_tomo_spec_displ_x_min(XSDataLength(0))
self.forceInstrument.set_tomo_spec_displ_x_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the number of slow motor steps (you will have n+1 points): "
).strip()
try:
self.slowMotorSteps = int(strtmp)
except ValueError:
self.slowMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_scan_ampl(
XSDataLength(self.slowMotorSteps))
self.forceInstrument.set_tomo_spec_displ_rotation_inc(
XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the index offset of your images: ").strip()
try:
self.indexOffset = int(strtmp)
except ValueError:
print("unable to understand what you said, skipping")
def createInputCharacterisationFromSubWedges(self):
self.DEBUG(
"EDPluginControlInterfacev1_3.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.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam(
).setApertureSize(XSDataLength(self.fApertureSize))
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)
def generateXSDataMOSFLMInputIndexing(_xsDataIndexingInput):
"""
Translation from XSDataIndexingInput to XSDataMOSFLMInputIndexing.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing")
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataExperimentalCondition = _xsDataIndexingInput.getExperimentalCondition(
)
xsDataCrystal = _xsDataIndexingInput.getCrystal()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
if (xsDataExperimentalCondition is None):
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(dBeamPositionX))
xsDataMOSFLMBeamPosition.setY(XSDataLength(dBeamPositionY))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(dWavelength))
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(dDistance))
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
strPath = xsDataImageFirst.getPath().getValue()
strFileName = os.path.basename(strPath)
strDirectory = os.path.dirname(strPath)
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFileName, 1)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFileName, "#")
xsDataMOSFLMInputIndexing.setTemplate(XSDataString(strMOSFLMTemplate))
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(strDirectory))
if (xsDataCrystal is not None):
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
xsDataStringName = xsDataSpaceGroup.getName()
if (xsDataStringName is not None):
xsDataMOSFLMInputIndexing.setSymmetry(
XSDataString(xsDataStringName.getValue()))
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth(
).getValue()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
for xsDataImage in xsDataImageList:
# Create the MOSFLM image object
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fImageOscillationStart = fGonioStatOscillationStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataMOSFLMImage.setRotationAxisStart(
XSDataAngle(fImageOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fImageOscillationStart +
fGonioStatOscillationRange))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputIndexing
def generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput):
"""
Translation from XSDataGeneratePredictionInput to XSDataMOSFLMInputGeneratePrediction.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction"
)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataIndexingSolutionSelected = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined(
)
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction(
)
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputGeneratePrediction.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setMosaicity(
xsDataCrystal.getMosaicity())
xsDataMOSFLMInputGeneratePrediction.setSymmetry(
xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
xsDataMOSFLMInputGeneratePrediction.setWavelength(
xsDataBeam.getWavelength())
xsDataMOSFLMInputGeneratePrediction.setDistance(
xsDataDetector.getDistance())
xsDataMOSFLMInputGeneratePrediction.setDirectory(
XSDataString(strDirectoryFirst))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
# The MOSFLM plugin can only handle one image
xsDataImage = xsDataSubWedge.getImage()[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
iImageNumber = xsDataImage.getNumber().getValue()
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFilenameFirst, iImageNumber)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputGeneratePrediction.setTemplate(
XSDataString(strMOSFLMTemplate))
xsDataMOSFLMImage = XSDataMOSFLMImage()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fOscillationStart + fOscillationRange))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputGeneratePrediction
def generateXSDataIndexingResult(_xsDataMOSFLMIndexingOutput,
_xsDataExperimentalCondition=None):
"""
Translation from XSDataMOSFLMIndexingOutput to XSDataIndexingResult.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataIndexingOutput")
xsDataMOSFLMBeamPositionRefined = _xsDataMOSFLMIndexingOutput.getRefinedBeam(
)
xsDataMOSFLMBeamPositionShift = _xsDataMOSFLMIndexingOutput.getBeamShift(
)
dDeviationAngular = _xsDataMOSFLMIndexingOutput.getDeviationAngular(
).getValue()
dDeviationPositional = _xsDataMOSFLMIndexingOutput.getDeviationPositional(
).getValue()
dMosaicityEstimation = _xsDataMOSFLMIndexingOutput.getMosaicityEstimation(
).getValue()
dDistanceRefined = _xsDataMOSFLMIndexingOutput.getRefinedDistance(
).getValue()
iSelectedSolution = _xsDataMOSFLMIndexingOutput.getSelectedSolutionNumber(
).getValue()
iSpotsTotal = _xsDataMOSFLMIndexingOutput.getSpotsTotal().getValue()
iSpotsUsed = _xsDataMOSFLMIndexingOutput.getSpotsUsed().getValue()
xsDataCellRefined = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getRefinedCell()
xsDataMatrixA = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getAMatrix()
xsDataMatrixU = _xsDataMOSFLMIndexingOutput.getRefinedNewmat(
).getUMatrix()
strSelectedSpaceGroupName = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroup(
).getValue()
iSelectedSpaceGroupNumber = _xsDataMOSFLMIndexingOutput.getSelectedSolutionSpaceGroupNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for possibleSolutions in _xsDataMOSFLMIndexingOutput.getPossibleSolutions(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(
XSDataString(possibleSolutions.getLattice().getValue()))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(possibleSolutions.getCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = possibleSolutions.getIndex().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolution.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolution):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
xsDataIndexingSolutionSelected.setPenalty(
XSDataFloat(possibleSolutions.getPenalty().getValue()))
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(strSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(
XSDataInteger(iSelectedSpaceGroupNumber))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellRefined)
xsDataCrystalSelected.setMosaicity(XSDataDouble(dMosaicityEstimation))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataMatrixA)
xsDataOrientation.setMatrixU(xsDataMatrixU)
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(xsDataMOSFLMBeamPositionShift.getX().getValue()))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(xsDataMOSFLMBeamPositionShift.getY().getValue()))
xsDataStatisticsIndexing.setSpotDeviationAngular(
XSDataAngle(dDeviationAngular))
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(dDeviationPositional))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iSpotsUsed))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iSpotsTotal))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getX().getValue()))
xsDataDetector.setBeamPositionY(
XSDataLength(xsDataMOSFLMBeamPositionRefined.getY().getValue()))
xsDataDetector.setDistance(XSDataLength(dDistanceRefined))
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataMOSFLMIndexingOutput.getPathToLogFile())
return xsDataIndexingResult
def getXSDataResultStrategy(self, _xsDataResultBest,
_xsDataExperimentalCondition, _xsDataSample):
xsDataResultStrategy = XSDataResultStrategy()
listXSDataBestCollectionPlan = _xsDataResultBest.getCollectionPlan()
for xsDataBestCollectionPlan in listXSDataBestCollectionPlan:
xsDataCollectionPlan = XSDataCollectionPlan()
xsDataCollectionStrategy = XSDataCollection()
xsDataBestStrategySummary = xsDataBestCollectionPlan.getStrategySummary(
)
xsDataDoubleTransmission = xsDataBestStrategySummary.getTransmission(
)
for xsDataBestCollectionRun in xsDataBestCollectionPlan.getCollectionRun(
):
xsDataSubWedge = XSDataSubWedge()
strXmlStringDataExperimentalCondition = _xsDataExperimentalCondition.marshal(
)
xsDataExperimentalCondition = XSDataExperimentalCondition.parseString(
strXmlStringDataExperimentalCondition)
xsDataExperimentalCondition.getBeam().setExposureTime(
xsDataBestCollectionRun.getExposureTime())
if (xsDataBestCollectionRun.getTransmission() is None):
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataDoubleTransmission)
else:
xsDataExperimentalCondition.getBeam().setTransmission(
xsDataBestCollectionRun.getTransmission())
xsDataExperimentalCondition.getDetector().setDistance(
xsDataBestStrategySummary.getDistance())
xsDataExperimentalCondition.getGoniostat(
).setRotationAxisStart(xsDataBestCollectionRun.getPhiStart())
xsDataExperimentalCondition.getGoniostat().setOscillationWidth(
xsDataBestCollectionRun.getPhiWidth())
fRotationAxisEnd = xsDataBestCollectionRun.getPhiStart(
).getValue(
) + xsDataBestCollectionRun.getNumberOfImages().getValue(
) * xsDataBestCollectionRun.getPhiWidth().getValue()
xsDataExperimentalCondition.getGoniostat().setRotationAxisEnd(
XSDataAngle(fRotationAxisEnd))
xsDataSubWedge.setExperimentalCondition(
xsDataExperimentalCondition)
xsDataSubWedge.setSubWedgeNumber(
xsDataBestCollectionRun.getCollectionRunNumber())
if xsDataBestCollectionRun.getCrystalPosition():
xsDataSubWedge.setAction(
XSDataString("Crystal position: %d" %
xsDataBestCollectionRun.
getCrystalPosition().getValue()))
else:
xsDataSubWedge.setAction(
xsDataBestCollectionRun.getAction())
xsDataCollectionStrategy.addSubWedge(xsDataSubWedge)
xsDataCollectionStrategy.setSample(_xsDataSample)
xsDataCollectionPlan.setCollectionStrategy(
xsDataCollectionStrategy)
xsDataStrategySummary = XSDataStrategySummary()
xsDataStrategySummary.setCompleteness(
xsDataBestStrategySummary.getCompleteness())
xsDataStrategySummary.setISigma(
xsDataBestStrategySummary.getISigma())
xsDataStrategySummary.setRankingResolution(
xsDataBestStrategySummary.getRankingResolution())
xsDataStrategySummary.setRedundancy(
xsDataBestStrategySummary.getRedundancy())
xsDataStrategySummary.setResolution(
xsDataBestStrategySummary.getResolution())
xsDataStrategySummary.setResolutionReasoning(
xsDataBestStrategySummary.getResolutionReasoning())
xsDataStrategySummary.setTotalDataCollectionTime(
xsDataBestStrategySummary.getTotalDataCollectionTime())
xsDataStrategySummary.setTotalExposureTime(
xsDataBestStrategySummary.getTotalExposureTime())
xsDataCollectionPlan.setStrategySummary(xsDataStrategySummary)
if xsDataBestCollectionPlan.getStatisticalPrediction() is not None:
xsDataStatisticsStrategy = XSDataStatisticsStrategy.parseString(
xsDataBestCollectionPlan.getStatisticalPrediction(
).marshal())
xsDataCollectionPlan.setStatistics(xsDataStatisticsStrategy)
xsDataCollectionPlan.setCollectionPlanNumber(
xsDataBestCollectionPlan.getCollectionPlanNumber())
xsDataResultStrategy.addCollectionPlan(xsDataCollectionPlan)
if _xsDataResultBest.getPathToLogFile() != None:
xsDataResultStrategy.setBestLogFile(
_xsDataResultBest.getPathToLogFile())
return xsDataResultStrategy
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 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 preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlGeneratePredictionv10.preProcess...")
xsDataGeneratePredictionInput = self.getDataInput()
xsDataSelectedIndexingSolution = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataExperimentalConditionRefined = xsDataSelectedIndexingSolution.getExperimentalConditionRefined(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
# List containing instances of all the generate prediction plugins
self.__listPluginGeneratePrediction = []
# Loop through all subwedges
iIndex = 0
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Then loop through all images in a sub wedge
for xsDataImage in xsDataImageList:
iIndex += 1
edPluginGeneratePrediction = self.loadPlugin(
self.__strPluginGeneratePredictionName, "%s-%02d" %
(self.__strPluginGeneratePredictionName, iIndex))
xsDataGeneratePredictionInput = XSDataGeneratePredictionInput()
xsDataGeneratePredictionInput.setSelectedIndexingSolution(
XSDataIndexingSolutionSelected.parseString(
xsDataSelectedIndexingSolution.marshal()))
xsDataCollectionNew = XSDataCollection()
xsDataSubWedgeNew = XSDataSubWedge()
xsDataSubWedgeNew.addImage(
XSDataImage.parseString(xsDataImage.marshal()))
xsDataSubWedgeNew.setExperimentalCondition(
XSDataExperimentalCondition.parseString(
xsDataSubWedge.getExperimentalCondition().marshal()))
# We must modify the rotationOscillationStart for the new subwedge
xsDataGoniostatNew = xsDataSubWedgeNew.getExperimentalCondition(
).getGoniostat()
fGoniostatRotationAxisStart = xsDataGoniostatNew.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostatNew.getOscillationWidth(
).getValue()
iImageNumber = xsDataImage.getNumber().getValue()
fGoniostatRotationAxisStartNew = fGoniostatRotationAxisStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataGoniostatNew.setRotationAxisStart(
XSDataAngle(fGoniostatRotationAxisStartNew))
#
xsDataCollectionNew.addSubWedge(xsDataSubWedgeNew)
xsDataGeneratePredictionInput.setDataCollection(
xsDataCollectionNew)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputGeneratePrediction = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput)
edPluginGeneratePrediction.setDataInput(
xsDataMOSFLMInputGeneratePrediction)
self.__listPluginGeneratePrediction.append(
edPluginGeneratePrediction)
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
strAbsolutePath = os.path.abspath(strPath)
dictHeader = self.readHeaderADSC(strPath)
if (dictHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : error when reading header from %s" % strAbsolutePath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(float(dictHeader[ "BEAM_CENTER_X" ])))
xsDataDetector.setBeamPositionY(XSDataLength(float(dictHeader[ "BEAM_CENTER_Y" ])))
xsDataDetector.setDistance(XSDataLength(float(dictHeader[ "DISTANCE" ])))
fPixelSize = float(dictHeader[ "PIXEL_SIZE" ])
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSize))
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSize))
if "TWOTHETA" in dictHeader.keys():
xsDataDetector.setTwoTheta(XSDataAngle(float(dictHeader[ "TWOTHETA" ])))
xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictHeader[ "HEADER_BYTES" ])))
xsDataDetector.setSerialNumber(XSDataString(dictHeader[ "DETECTOR_SN" ]))
xsDataDetector.setNumberPixelX(XSDataInteger(int(dictHeader[ "SIZE1" ])))
xsDataDetector.setNumberPixelY(XSDataInteger(int(dictHeader[ "SIZE2" ])))
xsDataDetector.setBin(XSDataString(dictHeader[ "BIN" ]))
xsDataDetector.setDataType(XSDataString(dictHeader[ "TYPE" ]))
xsDataDetector.setByteOrder(XSDataString(dictHeader[ "BYTE_ORDER" ]))
if "CCD_IMAGE_SATURATION" in dictHeader.keys():
xsDataDetector.setImageSaturation(XSDataInteger(int(dictHeader[ "CCD_IMAGE_SATURATION" ])))
# Determine type of detector...
iNoPixelsX = xsDataDetector.getNumberPixelX().getValue()
iNoPixelsY = xsDataDetector.getNumberPixelY().getValue()
if (iNoPixelsX == 2304 and iNoPixelsY == 2304):
xsDataDetector.setName(XSDataString("ADSC Q4"))
xsDataDetector.setType(XSDataString("q4"))
elif (iNoPixelsX == 1152 and iNoPixelsY == 1152):
xsDataDetector.setName(XSDataString("ADSC Q4 bin 2x2"))
xsDataDetector.setType(XSDataString("q4-2x"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("ADSC Q210"))
xsDataDetector.setType(XSDataString("q210"))
elif (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("ADSC Q210 bin 2x2"))
xsDataDetector.setType(XSDataString("q210-2x"))
elif (iNoPixelsX == 6144 and iNoPixelsY == 6144):
xsDataDetector.setName(XSDataString("ADSC Q315"))
xsDataDetector.setType(XSDataString("q315"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("ADSC Q315 bin 2x2"))
xsDataDetector.setType(XSDataString("q315-2x"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderADSCv10.process", "Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictHeader[ "WAVELENGTH" ])))
xsDataBeam.setExposureTime(XSDataTime(float(dictHeader[ "TIME" ])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictHeader[ "OSC_START" ])
fOscillationWidth = float(dictHeader[ "OSC_RANGE" ])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
strRotationAxis = None
if ("AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "AXIS" ]
elif ("OSC_AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "OSC_AXIS" ]
else:
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : Neither AXIS nor OSC_AXIS header item found."
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataGoniostat.setRotationAxis(XSDataString(strRotationAxis))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strAbsolutePath))
xsDataImage.setDate(XSDataString(dictHeader[ "DATE" ]))
strFileName = os.path.basename(strPath)
iImageNumber = EDUtilsImage.getImageNumber(strFileName)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.edPluginReadHeader.getDataOutput().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)
# if strUnit is None: strUnit = "A"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
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)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
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.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = xsd
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = 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)
self.edPluginPowderIntegration.executeSynchronous()
def testSetDataModelInput(self):
"""
"""
edPluginBest = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(
os.path.join(self.strDataPath, "XSConfiguration.xml"))
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv10 import XSDataBestInput
xsDataBestInput = XSDataBestInput()
from XSDataCommon import XSDataAbsorbedDoseRate
from XSDataCommon import XSDataFloat
from XSDataCommon import XSDataString
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
xsDataBestInput.setCrystalAbsorbedDoseRate(
XSDataAbsorbedDoseRate(0.22E+06))
xsDataBestInput.setCrystalShape(XSDataFloat(1))
xsDataBestInput.setCrystalSusceptibility(XSDataFloat(1.5))
xsDataBestInput.setDetectorType(XSDataString("q210-2x"))
xsDataBestInput.setBeamExposureTime(XSDataTime(1))
xsDataBestInput.setBeamMaxExposureTime(XSDataTime(10000))
xsDataBestInput.setBeamMinExposureTime(XSDataTime(0.1))
xsDataBestInput.setGoniostatMinRotationWidth(XSDataAngle(0.1))
xsDataBestInput.setGoniostatMaxRotationSpeed(XSDataSpeed(10))
xsDataBestInput.setAimedResolution(XSDataFloat(2))
xsDataBestInput.setAimedRedundancy(XSDataFloat(6.5))
xsDataBestInput.setAimedCompleteness(XSDataFloat(0.9))
xsDataBestInput.setAimedIOverSigma(XSDataFloat(3))
xsDataBestInput.setComplexity(XSDataString("min"))
fileDirectory = edPluginBest.getWorkingDirectory()
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataBestInput.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataBestInput.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
listBestFileContentHKL = []
listBestFileContentHKL.append(XSDataString(bestFileContentHKL))
xsDataBestInput.setBestFileContentHKL(listBestFileContentHKL)
xsDataBestInput.outputFile(self.strObtainedInputFile)
strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
strObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataBestInput.parseString(strExpectedInput)
xsDataInputObtained = XSDataBestInput.parseString(strObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
self.cleanUp(edPluginBest)
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 process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictEiger4MHeader = self.readHeaderEiger4M(strPath)
if (dictEiger4MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderEiger4Mv10.process : Cannot read header : %s" % strPath
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 2070
iNoPixelsY = 2167
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictEiger4MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictEiger4MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split()
fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX
fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictEiger4MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictEiger4MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictEiger4MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictEiger4MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictEiger4MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictEiger4MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictEiger4MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("EIGER 4M"))
xsDataDetector.setType(XSDataString("eiger4m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictEiger4MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictEiger4MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictEiger4MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictEiger4MHeader[ "Angle_increment" ].split(" ")[0])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
#
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
if "DateTime" in dictEiger4MHeader:
strTimeStamp = dictEiger4MHeader[ "DateTime" ]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'angle_alpha':
obj_ = XSDataAngle()
obj_.build(child_)
self.setAngle_alpha(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'angle_beta':
obj_ = XSDataAngle()
obj_.build(child_)
self.setAngle_beta(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'angle_gamma':
obj_ = XSDataAngle()
obj_.build(child_)
self.setAngle_gamma(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'length_a':
obj_ = XSDataLength()
obj_.build(child_)
self.setLength_a(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'length_b':
obj_ = XSDataLength()
obj_.build(child_)
self.setLength_b(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'length_c':
obj_ = XSDataLength()
obj_.build(child_)
self.setLength_c(obj_)
XSData.buildChildren(self, child_, nodeName_)
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 testIsSameExperimentalCondition(self):
edPluginSubWedgeMergev10 = self.createPlugin()
xsDataExperimentalConditionReference = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionSameAsReference = self.getTestExperimentalCondition(
)
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionSameAsReference), True)
xsDataExperimentalConditionDifferentExposureTime = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentExposureTime.getBeam(
).setExposureTime(XSDataTime(10.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentExposureTime), False)
xsDataExperimentalConditionDifferentWavelength = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentWavelength.getBeam().setWavelength(
XSDataWavelength(1.5))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentWavelength), False)
xsDataExperimentalConditionDifferentBeamPositionX = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentBeamPositionX.getDetector(
).setBeamPositionX(XSDataLength(20.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentBeamPositionX), False)
xsDataExperimentalConditionDifferentBeamPositionY = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentBeamPositionY.getDetector(
).setBeamPositionY(XSDataLength(20.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentBeamPositionY), False)
xsDataExperimentalConditionDifferentDistance = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentDistance.getDetector().setDistance(
XSDataLength(220.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentDistance), False)
xsDataExperimentalConditionDifferentName = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentName.getDetector().setName(
XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentName), False)
xsDataExperimentalConditionDifferentNumberPixelX = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentNumberPixelX.getDetector(
).setNumberPixelX(XSDataInteger(2))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentNumberPixelX), False)
xsDataExperimentalConditionDifferentNumberPixelY = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentNumberPixelY.getDetector(
).setNumberPixelY(XSDataInteger(2))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentNumberPixelY), False)
xsDataExperimentalConditionDifferentSerialNumber = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentSerialNumber.getDetector(
).setSerialNumber(XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentSerialNumber), False)
xsDataExperimentalConditionDifferentTwoTheta = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentTwoTheta.getDetector().setTwoTheta(
XSDataAngle(90.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentTwoTheta), False)
xsDataExperimentalConditionDifferentOscillationWidth = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentOscillationWidth.getGoniostat(
).setOscillationWidth(XSDataAngle(2.0))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentOscillationWidth), False)
xsDataExperimentalConditionDifferentRotationAxis = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentRotationAxis.getGoniostat(
).setRotationAxis(XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev10.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentRotationAxis), False)
