def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "dataCollectionId":
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "processDirectory":
obj_ = XSDataFile()
obj_.build(child_)
self.setProcessDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "doAnomAndNonanom":
obj_ = XSDataBoolean()
obj_.build(child_)
self.setDoAnomAndNonanom(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_): if child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'lower': obj_ = XSDataInteger() obj_.build(child_) self.setLower(obj_) elif child_.nodeType == Node.ELEMENT_NODE and \ nodeName_ == 'upper': obj_ = XSDataInteger() obj_.build(child_) self.setUpper(obj_) XSData.buildChildren(self, child_, nodeName_)
def parseLabelitScreenOutput(self, _strLabelitLogText):
"""
This method parses the labelit.screen log and populates the relevant
parts of the XSDataLabelitScreenOutput object which is then returned.
"""
self.DEBUG("EDPluginLabelitIndexingv1_1.parseLabelitLogText")
xsDataLabelitScreenOutput = None
iIndex = 0
listLogLines = _strLabelitLogText.split('\n')
bFoundLabelitIndexingResults = False
bContinue = True
while (bContinue):
if (listLogLines[iIndex].find("LABELIT Indexing results:") != -1):
bFoundLabelitIndexingResults = True
bContinue = False
else:
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
if (bFoundLabelitIndexingResults == False):
strErrorMessage = "EDPluginLabelitIndexingv1_1.parseLabelitLogText : Labelit log message: %s" % _strLabelitLogText
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
# We found some indexing results!
xsDataLabelitScreenOutput = XSDataLabelitScreenOutput()
iIndex += 1
strBeamDistanceMosaicity = listLogLines[iIndex]
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
',', '')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
'mm', ' ')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(
'=', ' ')
listStringBeamDistanceMosaicity = strBeamDistanceMosaicity.split()
fBeamX = float(listStringBeamDistanceMosaicity[3])
fBeamY = float(listStringBeamDistanceMosaicity[5])
xsDataLabelitScreenOutput.setBeamCentreX(XSDataLength(fBeamX))
xsDataLabelitScreenOutput.setBeamCentreY(XSDataLength(fBeamY))
fDistance = float(listStringBeamDistanceMosaicity[7])
xsDataLabelitScreenOutput.setDistance(XSDataLength(fDistance))
fMosaicity = float(listStringBeamDistanceMosaicity[11])
xsDataLabelitScreenOutput.setMosaicity(XSDataAngle(fMosaicity))
iIndex += 3
bContinue = True
bFoundSelectedSolution = False
while (bContinue):
xsDataLabelitScreenSolution = XSDataLabelitScreenSolution()
strLabelitSolution = listLogLines[iIndex]
listStringLabelitSolution = strLabelitSolution.split()
if (listStringLabelitSolution[0] == ":)"):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(True))
elif (listStringLabelitSolution[0] == ":("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
elif (listStringLabelitSolution[0] == ";("):
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
else:
# We have an error...
strErrorMessage = "Indexing with labelit.screen failed! Log file:"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.ERROR(_strLabelitLogText)
self.addErrorMessage(_strLabelitLogText)
self.setFailure()
bContinue = False
if bContinue:
iSolutionNumber = int(listStringLabelitSolution[1])
xsDataLabelitScreenSolution.setSolutionNumber(
XSDataInteger(iSolutionNumber))
fMetricFitValue = float(listStringLabelitSolution[2])
xsDataLabelitScreenSolution.setMetricFitValue(
XSDataDouble(fMetricFitValue))
strMetricFitCode = listStringLabelitSolution[3]
xsDataLabelitScreenSolution.setMetricFitCode(
XSDataString(strMetricFitCode))
fRMSD = float(listStringLabelitSolution[4])
xsDataLabelitScreenSolution.setRmsd(XSDataLength(fRMSD))
iNumberOfSpots = int(listStringLabelitSolution[5])
xsDataLabelitScreenSolution.setNumberOfSpots(
XSDataInteger(iNumberOfSpots))
strCrystalSystem = listStringLabelitSolution[6]
strBravaisLattice = listStringLabelitSolution[7]
xsDataLabelitScreenSolution.setCrystalSystem(
XSDataString(strCrystalSystem))
xsDataLabelitScreenSolution.setBravaisLattice(
XSDataString(strBravaisLattice))
xsDataCell = XSDataCell()
xsDataCell.setLength_a(
XSDataLength(float(listStringLabelitSolution[8])))
xsDataCell.setLength_b(
XSDataLength(float(listStringLabelitSolution[9])))
xsDataCell.setLength_c(
XSDataLength(float(listStringLabelitSolution[10])))
xsDataCell.setAngle_alpha(
XSDataAngle(float(listStringLabelitSolution[11])))
xsDataCell.setAngle_beta(
XSDataAngle(float(listStringLabelitSolution[12])))
xsDataCell.setAngle_gamma(
XSDataAngle(float(listStringLabelitSolution[13])))
xsDataLabelitScreenSolution.setUnitCell(xsDataCell)
iVolume = int(listStringLabelitSolution[14])
xsDataLabelitScreenSolution.setVolume(
XSDataInteger(iVolume))
# Find the selected solution
if (bFoundSelectedSolution == False):
if (xsDataLabelitScreenSolution.getHappy().getValue()
== True):
# Check if forced space group
if self.__strForcedSpaceGroup == None:
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(
XSDataInteger(iSolutionNumber))
else:
listBravaisLattice = self.getBravaisLatticeFromSpaceGroup(
self.__strForcedSpaceGroup)
for strPossibleBravaisLattice in listBravaisLattice:
if strBravaisLattice == strPossibleBravaisLattice:
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.setSelectedSolutionNumber(
XSDataInteger(iSolutionNumber))
xsDataLabelitScreenOutput.addLabelitScreenSolution(
xsDataLabelitScreenSolution)
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
return xsDataLabelitScreenOutput
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess")
# Load the plugins
self._edPluginControlIndexingIndicators = self.loadPlugin(self._strPluginControlIndexingIndicators, \
"Indexing")
self._edPluginControlIndexingLabelit = self.loadPlugin(self._strPluginControlIndexingLabelit, \
"IndexingLabelit")
self._edPluginExecEvaluationIndexingMOSFLM = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionMOSFLM")
self._edPluginExecEvaluationIndexingLABELIT = self.loadPlugin(self._strPluginExecEvaluationIndexing, \
"IndexingEvalualtionLABELIT")
self._edPluginControlGeneratePrediction = self.loadPlugin(self._strPluginControlGeneratePrediction, \
"GeneratePrediction")
self._edPluginControlIntegration = self.loadPlugin(self._strPluginControlIntegration, \
"Integration")
self._edPluginControlXDSGenerateBackgroundImage = self.loadPlugin(self._strPluginControlXDSGenerateBackgroundImage, \
"ControlXDSGenerateBackgroundImage")
self._edPluginControlStrategy = self.loadPlugin(self._strPluginControlStrategy, \
"Strategy")
if (self._edPluginControlIndexingIndicators is not None):
self.DEBUG("EDPluginControlCharacterisationv1_3.preProcess: " +
self._strPluginControlIndexingIndicators +
" Found... setting Data Input")
# create Data Input for indexing
xsDataInputCharacterisation = self.getDataInput()
self._xsDataCollection = xsDataInputCharacterisation.getDataCollection(
)
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataFirstSubWedge = self._xsDataCollection.getSubWedge()[0]
xsDataBeam = xsDataFirstSubWedge.getExperimentalCondition(
).getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self._fMinTransmission:
strWarningMessageBanner = "^" * 80
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.warning(strWarningMessageBanner)
self.warning(strWarningMessage1)
self.warning(strWarningMessage2)
self.warning(strWarningMessageBanner)
self.addWarningMessage(strWarningMessageBanner)
self.addWarningMessage(strWarningMessage1)
self.addWarningMessage(strWarningMessage2)
self.addWarningMessage(strWarningMessageBanner)
xsDataCrystal = None
xsDataSubWedgeList = self._xsDataCollection.getSubWedge()
if ((xsDataSubWedgeList is None) or (xsDataSubWedgeList == [])):
strError = "EDPluginControlCharacterisationv1_3.preProcess: No subwedges in input data."
self.ERROR(strError)
self.setFailure()
else:
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
# Fix for bug 431: if the flux is zero raise an error
xsDataDoubleFlux = xsDataExperimentalCondition.getBeam(
).getFlux()
if (xsDataDoubleFlux is not None):
if (xsDataDoubleFlux.getValue() < 0.1):
strErrorMessage = "Input flux is negative or close to zero. Execution of characterisation aborted."
self.ERROR(strErrorMessage)
self.addErrorMessage(
"EDPluginControlCharacterisationv1_3.preProcess ERROR: "
+ strErrorMessage)
#self.addComment(strErrorMessage)
self.setFailure()
xsDataDiffractionPlan = self._xsDataCollection.getDiffractionPlan(
)
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup(
)
if (xsDataStringForcedSpaceGroup is not None):
self._xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
self._xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCollection, "dataCollection")
if self._xsDataCrystal is not None:
self._edPluginControlIndexingIndicators.setDataInput(
self._xsDataCrystal, "crystal")
# Populate characterisation object
self._xsDataResultCharacterisation = XSDataResultCharacterisation(
)
self._xsDataResultCharacterisation.setDataCollection(
XSDataCollection.parseString(
self._xsDataCollection.marshal()))
# Load the thumbnail plugins
for subWedge in xsDataInputCharacterisation.dataCollection.subWedge:
for image in subWedge.image:
edPluginJpeg = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
jpegFilename = os.path.splitext(
os.path.basename(image.path.value))[0] + ".jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
jpegFilename)))
edPluginJpeg.dataInput = xsDataInputMXThumbnail
edPluginThumnail = self.loadPlugin(
self._strPluginGenerateThumbnailName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = XSDataFile(image.path)
xsDataInputMXThumbnail.height = XSDataInteger(256)
xsDataInputMXThumbnail.width = XSDataInteger(256)
thumbnailFilename = os.path.splitext(
os.path.basename(
image.path.value))[0] + ".thumbnail.jpg"
xsDataInputMXThumbnail.outputPath = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
thumbnailFilename)))
edPluginThumnail.dataInput = xsDataInputMXThumbnail
self._listPluginGenerateThumbnail.append(
(image, edPluginJpeg, edPluginThumnail))
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 = 4150
iNoPixelsY = 4371
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 16M"))
xsDataDetector.setType(XSDataString("eiger16m"))
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 makeXML(self, filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
"""
self.header = None
dirname, basename = os.path.split(filename)
if not basename.startswith(self.prefix):
return
if self.normalizedSuffix and basename.endswith(self.normalizedSuffix):
return
if basename.startswith(self.flatPrefix):
return
if not basename.endswith(self.suffix):
return
if self.fScaleData:
fScaleData = self.fScaleData
else:
fScaleData = self.getNbFrames(filename)
if not fScaleData:
fScaleData = 1.0
if self.fScaleDark:
fScaleDark = self.fScaleDark
else:
fScaleDark = self.getNbFrames(self.darks[0]["path"])
if not fScaleDark:
fScaleDark = 1.0
if isinstance(self.reference, int):
reference = self.reference
else:
reference = -1
xsd = XSDataInputFullFieldXAS(
HDF5File=XSDataFile(path=XSDataString(self.HDF5)),
internalHDF5Path=XSDataString(self.internalHdf5),
measureOffset=self.getXSDMeasureOffset(),
dark=self.getXsdDark(),
reference=XSDataInteger(reference),
data=[
XSDataImageExt(path=XSDataString(filename),
exposureTime=XSDataTime(
self.getExposureTime(filename)))
],
dataScaleFactor=XSDataDouble(fScaleData),
darkScaleFactor=XSDataDouble(fScaleDark),
)
if self.dontAlign:
xsd.dontAlign = XSDataBoolean(self.dontAlign)
extendedPrefix = ""
number = ""
started = False
if self.lstSubscanSize:
subScanDigit = []
for i in basename[len(self.prefix):]:
if started and i == "_":
if len(number) > 0:
subScanDigit.append(number)
number = ""
continue
if started and not i.isdigit():
if number:
subScanDigit.append(number)
number = ""
break
if not started:
if i.isdigit():
started = True
else:
extendedPrefix += i
if started:
number += i
if not subScanDigit:
print("ERROR: no index guessed !!!")
return ""
elif len(subScanDigit) == 1:
index = int(subScanDigit[0])
else: # len(subScanDigit) > 1:
index = 0
for i in range(int(subScanDigit[0])):
index += self.lstSubscanSize[i]
index += int(subScanDigit[1])
extendedPrefix += "_".join(subScanDigit[:2])
else:
for i in basename[len(self.prefix):]:
extendedPrefix += i
if started and not i.isdigit():
break
if not started and i.isdigit():
started = True
if started:
number += i
index = int(number)
xsd.index = XSDataInteger(index)
if self.normalizedSuffix:
pr = os.path.splitext(os.path.abspath(filename))[0]
xsd.saveNormalized = XSDataFile(
path=XSDataString(pr + self.normalizedSuffix))
energy = self.getEnergy(filename)
if energy is not None:
xsd.energy = XSDataDouble(energy)
flatprefix = self.flatPrefix + extendedPrefix
listFlats = []
for oneFile in os.listdir(dirname):
if oneFile.startswith(flatprefix) and oneFile.endswith(
self.suffix):
oneCompleteFile = os.path.abspath(
os.path.join(dirname, oneFile))
xsdFileFlat1 = XSDataImageExt(
path=XSDataString(oneCompleteFile),
exposureTime=XSDataTime(
self.getExposureTime(oneCompleteFile)))
listFlats.append(xsdFileFlat1)
xsd.flat = listFlats
if len(listFlats) != 2:
EDVerbose.WARNING("Not exactly 2 flats were found:" +
" ".join([a.path.value for a in listFlats]))
EDVerbose.WARNING("Those are the flat prefix ans suffix: %s\t%s" %
(flatprefix, self.suffix))
if self.fScaleFlat:
fScaleFlat = self.fScaleFlat
else:
fScaleFlat = self.getNbFrames(oneCompleteFile)
if not fScaleFlat:
fScaleFlat = 1.0
xsd.flatScaleFactor = XSDataDouble(fScaleFlat)
return xsd.marshal()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlSaxsAnalysisv1_1.process")
if self.autoRg is None:
self.edPluginAutoRg = self.loadPlugin(self.cpAutoRg)
self.edPluginAutoRg.dataInput = XSDataInputAutoRg(inputCurve=[self.dataInput.scatterCurve])
self.edPluginAutoRg.connectSUCCESS(self.doSuccessRg)
self.edPluginAutoRg.connectFAILURE(self.doFailureRg)
self.edPluginAutoRg.executeSynchronous()
if self.autoRg is None:
self.setFailure()
if self.isFailure():
return
self.edPluginDatGnom = self.loadPlugin(self.cpDatGnom)
self.edPluginDatGnom.dataInput = XSDataInputDatGnom(inputCurve=self.dataInput.scatterCurve,
output=XSDataFile(XSDataString(self.gnomFile)),
rg=self.autoRg.rg,
skip=XSDataInteger(self.autoRg.firstPointUsed.value - 1))
self.edPluginDatGnom.connectSUCCESS(self.doSuccessGnom)
self.edPluginDatGnom.connectFAILURE(self.doFailureGnom)
self.edPluginDatGnom.executeSynchronous()
if self.gnom is None:
return
self.edPluginDatPorod = self.loadPlugin(self.cpDatPorod)
self.edPluginDatPorod.dataInput = XSDataInputDatPorod(gnomFile=XSDataFile(XSDataString(self.gnomFile)))
self.edPluginDatPorod.connectSUCCESS(self.doSuccessPorod)
self.edPluginDatPorod.connectFAILURE(self.doFailurePorod)
self.edPluginDatPorod.execute()
if self.dataInput.graphFormat:
ext = self.dataInput.graphFormat.value
if not ext.startswith("."):
ext = "." + ext
plt = sys.modules.get("matplotlib.pyplot")
try:
guinierfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-Guinier" + ext)
# guinierplot = guinierPlot(self.scatterFile, unit="nm",
# filename=guinierfile, format=ext[1:])
guinierplot = guinierPlot(self.scatterFile, unit="nm",
filename=guinierfile, format=ext[1:], first_point=self.autoRg.firstPointUsed.value,
last_point=self.autoRg.lastPointUsed.value)
guinierplot.clf()
if plt:
plt.close(guinierplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in guinierplot: %s" % error)
else:
self.xsDataResult.guinierPlot = XSDataFile(XSDataString(guinierfile))
try:
kratkyfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-Kratky" + ext)
kratkyplot = kartkyPlot(self.scatterFile, unit="nm",
filename=kratkyfile, format=ext[1:])
kratkyplot.clf()
if plt:
plt.close(kratkyplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in kratkyplot: %s" % error)
else:
self.xsDataResult.kratkyPlot = XSDataFile(XSDataString(kratkyfile))
if self.autoRg is not None:
if self.autoRg.i0.value > 0 and self.autoRg.rg.value > 0:
try:
kratkyRgfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-KratkyRg" + ext)
kratkyRgplot = kratkyRgPlot(self.scatterFile, self.autoRg.i0.value, self.autoRg.rg.value,
filename=kratkyRgfile, format=ext[1:])
kratkyRgplot.clf()
if plt:
plt.close(kratkyRgplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in kratkyRgplot: %s" % error)
else:
self.xsDataResult.kratkyRgPlot = XSDataFile(XSDataString(kratkyRgfile))
if self.autoRg is not None and self.rti is not None:
if self.autoRg.i0.value > 0 and self.rti.vc.value > 0:
try:
kratkyVcfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-KratkyVc" + ext)
kratkyVcplot = kratkyVcPlot(self.scatterFile, self.autoRg.i0.value, self.rti.vc.value,
filename=kratkyVcfile, format=ext[1:])
kratkyVcplot.clf()
if plt:
plt.close(kratkyVcplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in kratkyVcplot: %s" % error)
else:
self.xsDataResult.kratkyVcPlot = XSDataFile(XSDataString(kratkyVcfile))
try:
scatterplotfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-scattering" + ext)
scatterplot = scatterPlot(self.scatterFile, unit="nm", gnomfile=self.gnomFile,
filename=scatterplotfile, format=ext[1:])
scatterplot.clf()
if plt:
plt.close(scatterplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in scatterplot: %s" % error)
else:
self.xsDataResult.scatterPlot = XSDataFile(XSDataString(scatterplotfile))
try:
densityplotfile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.scatterFile).split(".")[0] + "-density" + ext)
densityplot = densityPlot(gnomfile=self.gnomFile, unit="nm",
filename=densityplotfile, format=ext[1:])
densityplot.clf()
if plt:
plt.close(densityplot)
except Exception as error:
self.ERROR("EDPluginControlSaxsAnalysisv1_1 in scatterplot: %s" % error)
else:
self.xsDataResult.densityPlot = XSDataFile(XSDataString(densityplotfile))
gc.collect()
self.synchronizePlugins()
def create_autoproc_input(self, event, params):
"""
Descript. :
"""
WAIT_XDS_TIMEOUT = 20
WAIT_XDS_RESOLUTION = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(autoproc_path,
"edna-autoproc-input-%s" % \
file_name_timestamp)
autoproc_output_file_name = os.path.join(autoproc_path,
"edna-autoproc-results-%s" % \
file_name_timestamp)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(
XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if type(space_group) != int and len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
#Maybe we have to check if directory is there. Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.info('MAXIVAutoprocessing: Waiting for XDS.INP file: %s' %
autoproc_xds_filename)
while not xds_appeared and time.time(
) - wait_xds_start < WAIT_XDS_TIMEOUT:
if os.path.exists(autoproc_xds_filename
) and os.stat(autoproc_xds_filename).st_size > 0:
xds_appeared = True
logging.debug('MAXIVAutoprocessing: XDS.INP file is there, size={0}'.\
format(os.stat(autoproc_xds_filename).st_size))
else:
os.system("ls %s> /dev/null" %
(os.path.dirname(autoproc_path)))
gevent.sleep(WAIT_XDS_RESOLUTION)
if not xds_appeared:
logging.error('MAXIVAutoprocessing: XDS.INP file ({0}) failed to appear after {1} seconds'.\
format(autoproc_xds_filename, WAIT_XDS_TIMEOUT))
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True
def generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \
_xsDataExperimentalCondition=None, _strSymopFileName=None):
EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName))
if not _strSymopFileName is None:
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName, _strSymopFileName)))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(_xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(_xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX().getValue()
fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
#xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected))
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(_xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(_xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(_xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
def getDataCollectionOutputDataFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
# SubWedges
xsTablesCollectionStrategy = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "data_collection_strategy")
iCollectionPlanNumber = 1
for xsTableCollectionStrategy in xsTablesCollectionStrategy:
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsCollectionRunList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "collection_run")
iCollectionRunNumber = 1
for xsCollectionRunItemList in xsCollectionRunList:
xsDataCollectionRun = self.collectionRunItemListToCollectionRun(
xsCollectionRunItemList, iCollectionRunNumber)
xsDataBestCollectionPlan.addCollectionRun(xsDataCollectionRun)
iCollectionRunNumber = iCollectionRunNumber + 1
# Strategy Summary
xsStrategySummaryItemList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "summary")
xsDataStrategySummary = self.strategySummaryItemListToStrategySummary(
xsStrategySummaryItemList[0])
# Ranking Resolution
# Not part of strategySummaryItemListToStrategySummary method since it is in the general_form part
xsTableGeneralInform = EDUtilsTable.getTableFromTables(
_xsDataDnaTables, "general_inform")
xsRankingResolutionItemList = EDUtilsTable.getListsFromTable(
xsTableGeneralInform, "ranking_resolution")
xsItemRankingResolution = EDUtilsTable.getItemFromList(
xsRankingResolutionItemList[0], "dmin")
fRankingResolution = float(xsItemRankingResolution.getValueOf_())
xsDataStrategySummary.setRankingResolution(
XSDataDouble(fRankingResolution))
xsDataBestCollectionPlan.setStrategySummary(xsDataStrategySummary)
# Satistics
xsTablesStatisticalPrediction = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "statistical_prediction")
for xsTableStatisticalPrediction in xsTablesStatisticalPrediction:
if (xsTableStatisticalPrediction.getIndex() ==
xsTableCollectionStrategy.getIndex()):
xsResolutionBinList = EDUtilsTable.getListsFromTable(
xsTableStatisticalPrediction, "resolution_bin")
xsDataStatisticalPrediction = XSDataBestStatisticalPrediction(
)
for xsResolutionBinItemList in xsResolutionBinList:
xsDataResolutionBin = self.resolutionBinItemListToResolutionBin(
xsResolutionBinItemList)
xsDataStatisticalPrediction.addResolutionBin(
xsDataResolutionBin)
xsDataBestCollectionPlan.setStatisticalPrediction(
xsDataStatisticalPrediction)
xsDataBestCollectionPlan.setCollectionPlanNumber(
XSDataInteger(iCollectionPlanNumber))
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
iCollectionPlanNumber = iCollectionPlanNumber + 1
# Fix the order of the collection plans - then low resolution pass should be the first one
listCollectionPlan = xsDataResultBest.getCollectionPlan()
if (len(listCollectionPlan) > 1):
bIsModified = False
for xsDataCollectionPlan in listCollectionPlan:
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
strReasoning = xsDataStrategySummary.getResolutionReasoning(
).getValue()
if ((strReasoning.find("Low-resolution") != -1)
and xsDataCollectionPlan.getCollectionPlanNumber(
).getValue() != 1):
listCollectionPlan.remove(xsDataCollectionPlan)
listCollectionPlan.insert(0, xsDataCollectionPlan)
bIsModified = True
if (bIsModified):
iCollectionPlanNumber = 1
for xsDataCollectionPlan in listCollectionPlan:
xsDataCollectionPlan.setCollectionPlanNumber(
XSDataInteger(iCollectionPlanNumber))
iCollectionPlanNumber = iCollectionPlanNumber + 1
return xsDataResultBest
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataCollectionId':
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'processDirectory':
obj_ = XSDataFile()
obj_.build(child_)
self.setProcessDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'doAnomAndNonanom':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setDoAnomAndNonanom(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'spaceGroup':
obj_ = XSDataString()
obj_.build(child_)
self.setSpaceGroup(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'unitCell':
obj_ = XSDataString()
obj_.build(child_)
self.setUnitCell(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'startFrame':
obj_ = XSDataInteger()
obj_.build(child_)
self.setStartFrame(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'endFrame':
obj_ = XSDataInteger()
obj_.build(child_)
self.setEndFrame(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataFloat
x = XSDataBoolean(True)
print x.value
print x.marshal()
x = XSDataBoolean(False)
print x.value
print x.marshal()
x = XSDataBoolean('true')
print x.value
print x.marshal()
x = XSDataBoolean('False')
print x.value
print x.marshal()
x = XSDataBoolean(0)
print x.value
print x.marshal()
x = XSDataBoolean(1)
print x.value
print x.marshal()
x = XSDataBoolean(2)
print x.value
print x.marshal()
y = XSDataFloat('this is not a float')
print y.value
print y.marshal()
z = XSDataInteger('this is not an integer')
print z.value
print z.marshal()
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hdf5ImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setHdf5ImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hdf5File':
obj_ = XSDataFile()
obj_.build(child_)
self.setHdf5File(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'forcedOutputDirectory':
obj_ = XSDataFile()
obj_.build(child_)
self.setForcedOutputDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'forcedOutputImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setForcedOutputImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'startImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setStartImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'endImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setEndImageNumber(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_5.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen(
"Image quality indicators batch size: {0}".format(batchSize))
# Check if we should do distlSignalStrength:
bDoDistlSignalStrength = True
if self.dataInput.doDistlSignalStrength is not None:
if not self.dataInput.doDistlSignalStrength.value:
bDoDistlSignalStrength = False
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Check if fast mesh (for HDF5)
isFastMesh = False
if self.dataInput.fastMesh:
isFastMesh = self.dataInput.fastMesh.value
# Loop through all the incoming reference images
if len(self.dataInput.image) == 0:
directory = self.dataInput.directory.path.value
template = self.dataInput.template.value
startNo = self.dataInput.startNo.value
endNo = self.dataInput.endNo.value
listXSDataImage = []
for index in range(startNo, endNo + 1):
imageName = template.replace("####", "{0:04d}".format(index))
imagePath = os.path.join(directory, imageName)
xsDataImage = XSDataImage(path=XSDataString(imagePath),
number=XSDataInteger(index))
listXSDataImage.append(xsDataImage)
else:
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPluginDistl = []
listPluginDozor = []
listOfImagesInBatch = []
listOfAllBatches = []
indexBatch = 0
listH5FilePath = []
# Process data in batches
for xsDataImage in listXSDataImage:
listOfImagesInBatch.append(xsDataImage.copy())
if len(listOfImagesInBatch) == batchSize:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
if len(listOfImagesInBatch) > 0:
listOfAllBatches.append(listOfImagesInBatch)
listOfImagesInBatch = []
# Loop over batches
for listOfImagesInBatch in listOfAllBatches:
# First wait for images
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# If Eiger, just wait for the h5 file
if strPathToImage.endswith(".h5"):
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(
strPathToImage,
batchSize=batchSize,
isFastMesh=isFastMesh)
# print(h5FilePath)
# print(hdf5ImageNumber)
if not h5DataFilePath in listH5FilePath:
self.screen(
"ID30a3 Eiger data, waiting for master and data files..."
)
listH5FilePath.append(h5DataFilePath)
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(h5DataFilePath))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen(
"Waiting for file {0}".format(h5DataFilePath))
self.DEBUG("Wait file timeOut set to %f" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
# hdf5FilePath = strPathToImage.replace(".cbf", ".h5")
time.sleep(1)
if not os.path.exists(h5DataFilePath):
strError = "Time-out while waiting for image %s" % h5DataFilePath
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if not os.path.exists(strPathToImage):
# self.screen("Waiting for file {0}".format(strPathToImage))
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(
XSDataString(strPathToImage))
xsDataInputMXWaitFile.setSize(
XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.screen("Wait file timeOut set to %.0f s" %
self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(
xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(strPathToImage):
strError = "Time-out while waiting for image %s" % strPathToImage
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
if not self.isFailure():
strPathToFirstImage = listOfImagesInBatch[0].path.value
if strPathToImage.endswith(".h5"):
indexLoop = 1
continueLoop = True
while continueLoop:
directory = os.path.dirname(strPathToFirstImage)
firstImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[0].path.value)
lastImage = EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = XSDataFile(
listOfImagesInBatch[0].path)
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(1)
xsDataInputH5ToCBF.startImageNumber = XSDataInteger(
firstImage)
xsDataInputH5ToCBF.endImageNumber = XSDataInteger(
lastImage)
xsDataInputH5ToCBF.forcedOutputDirectory = XSDataFile(
XSDataString(directory))
edPluginH5ToCBF = self.loadPlugin(
"EDPluginH5ToCBFv1_1")
edPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
edPluginH5ToCBF.execute()
edPluginH5ToCBF.synchronize()
outputCBFFileTemplate = edPluginH5ToCBF.dataOutput.outputCBFFileTemplate
if outputCBFFileTemplate is not None:
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:06d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)))
strPathToImage = os.path.join(
directory, lastCbfFile)
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
# Rename all images
for image in listOfImagesInBatch:
image.path.value = image.path.value.replace(
".h5", ".cbf")
imageNumber = EDUtilsImage.getImageNumber(
image.path.value)
oldPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:06d}".format(imageNumber)))
newPath = os.path.join(
directory,
outputCBFFileTemplate.path.value.
replace("######",
"{0:04d}".format(imageNumber)))
os.rename(oldPath, newPath)
lastCbfFile = outputCBFFileTemplate.path.value.replace(
"######", "{0:04d}".format(
EDUtilsImage.getImageNumber(
listOfImagesInBatch[-1].path.value)
))
strPathToImage = os.path.join(
directory, lastCbfFile)
self.screen(
"Image has been converted to CBF file: {0}"
.format(strPathToImage))
continueLoop = False
# print(continueLoop)
if continueLoop:
self.screen(
"Still waiting for converting to CBF file: {0}"
.format(strPathToImage))
indexLoop += 1
time.sleep(5)
if indexLoop > 10:
continueLoop = False
for image in listOfImagesInBatch:
strPathToImage = image.path.value
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
xsDataImageNew.number = XSDataInteger(
EDUtilsImage.getImageNumber(image.path.value))
edPluginPluginExecImageQualityIndicator = None
if bDoDistlSignalStrength:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(
xsDataImageNew)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listPluginDistl.append(
(xsDataImageNew.copy(),
edPluginPluginExecImageQualityIndicator))
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor, "ControlDozor_{0}".format(
os.path.splitext(
os.path.basename(strPathToFirstImage))[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listOfImagesInBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
len(listOfImagesInBatch))
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append(
(edPluginControlDozor, list(listOfImagesInBatch)))
if not self.isFailure():
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for (xsDataImage,
edPluginPluginExecImageQualityIndicator) in listPluginDistl:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.image = xsDataImage.copy()
if edPluginPluginExecImageQualityIndicator is not None:
edPluginPluginExecImageQualityIndicator.synchronize()
if edPluginPluginExecImageQualityIndicator.dataOutput is not None:
if edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
# Check that we got at least one result
if len(edPluginControlDozor.dataOutput.imageDozor) == 0:
# Run the dozor plugin again, this time synchronously
firstImage = os.path.basename(listBatch[0].path.value)
lastImage = os.path.basename(listBatch[-1].path.value)
self.screen(
"No dozor results! Re-executing Dozor for images {0} to {1}"
.format(firstImage, lastImage))
time.sleep(5)
edPluginControlDozor = self.loadPlugin(
self.strPluginNameControlDozor,
"ControlDozor_reexecution_{0}".format(
os.path.splitext(firstImage)[0]))
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(
image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(
batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.executeSynchronous()
for imageDozor in edPluginControlDozor.dataOutput.imageDozor:
for xsDataImageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if xsDataImageQualityIndicators.image.path.value == imageDozor.image.path.value:
xsDataImageQualityIndicators.dozor_score = imageDozor.mainScore
xsDataImageQualityIndicators.dozorSpotFile = imageDozor.spotFile
if imageDozor.spotFile is not None:
if os.path.exists(
imageDozor.spotFile.path.value):
numpyArray = numpy.loadtxt(
imageDozor.spotFile.path.value,
skiprows=3)
xsDataImageQualityIndicators.dozorSpotList = XSDataString(
base64.b64encode(
numpyArray.tostring()))
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[0]))
if len(numpyArray.shape) > 1:
xsDataImageQualityIndicators.addDozorSpotListShape(
XSDataInteger(numpyArray.shape[1]))
xsDataImageQualityIndicators.dozorSpotsIntAver = imageDozor.spotsIntAver
xsDataImageQualityIndicators.dozorSpotsResolution = imageDozor.spotsResolution
xsDataImageQualityIndicators.dozorVisibleResolution = imageDozor.visibleResolution
if self.xsDataResultControlImageQualityIndicators.inputDozor is None:
if edPluginControlDozor.dataOutput.inputDozor is not None:
self.xsDataResultControlImageQualityIndicators.inputDozor = XSDataDozorInput(
).parseString(
edPluginControlDozor.dataOutput.
inputDozor.marshal())
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.dataInput.doUploadToIspyb is not None and self.dataInput.doUploadToIspyb.value:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
# Check that we have dozor_score from all images:
has_dozor_score = True
for imageQualityIndicators in self.xsDataResultControlImageQualityIndicators.imageQualityIndicators:
if imageQualityIndicators.dozor_score is None:
has_dozor_score = False
if has_dozor_score:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.dozor_score.value)
else:
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators:
imageQualityIndicators.totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[
-5:]:
if xsDataResultControlImageQualityIndicator.dozor_score.value > 1:
xsDataInputReadImageHeader = XSDataInputReadImageHeader(
)
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path
)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
edPluginLabelitIndexing = self.loadPlugin(
self.strIndexingLabelitPluginName)
xsDataInputLabelitIndexing = XSDataInputLabelitIndexing(
)
xsDataInputLabelitIndexing.image.append(
XSDataImage(
xsDataResultControlImageQualityIndicator.
image.path))
edPluginLabelitIndexing.setDataInput(
xsDataInputLabelitIndexing)
self.listPluginLabelit.append([
edPluginLabelitIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginLabelitIndexing.execute()
for tupleLabelit in self.listPluginLabelit:
edPluginLabelitIndexing = tupleLabelit[0]
xsDataResultControlImageQualityIndicator = tupleLabelit[1]
edPluginLabelitIndexing.synchronize()
if not edPluginLabelitIndexing.isFailure(
) and edPluginLabelitIndexing.dataOutput is not None:
xsDataResultLabelitIndexing = edPluginLabelitIndexing.getDataOutput(
)
xsDataIndexingResult = EDHandlerXSDataPhenixv1_1.generateXSDataIndexingResult(
xsDataResultLabelitIndexing)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_2.process")
xsdwf = XSDataInputWaitMultiFile(
timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
shutil.copyfile(self.lstInput[0].path.value,
self.dataInput.mergedCurve.path.value)
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity
is not None):
if self.absoluteFidelity is not None:
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[0], self.lstInput[1]])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" %
(idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(
self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(
inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(
self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(
self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity
is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity) and (self.dictSimilarities[
(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None):
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
if (self.dictSimilarities[(0, idx)] >=
self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) +
"\n".join([
"%s: %s" %
(key, self.dictSimilarities[key])
for key in self.dictSimilarities
]))
if (self.dictSimilarities[(idx - 1, idx)] >=
self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(
self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.lstSummary.append("WARNING: " + self.strRadiationDamage)
self.lstSummary.append("Merging files: " + " ".join(
[os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value,
self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(
self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
#outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(
self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(
self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
self.dictAve[self.tKey] = self.dataInput.mergedCurve
if len(self.tKey) == 3 and (self.tKey[0], self.tKey[1],
0.0) in self.dictAve:
#try to subtract buffer automatically
bufferKey = (self.tKey[0], self.tKey[1], 0.0)
bufferPath = self.dictAve[bufferKey]
if self.strSubFile is None:
self.strSubFile = self.strMergedFile.replace(
"_ave.dat", "_sub.dat")
if self.strMergedFile == self.strSubFile:
self.strSubFile = None
return
xsdSubFile = XSDataFile(XSDataString(self.strSubFile))
xsdSub = XSDataInputDatop(
inputCurve=[self.dataInput.mergedCurve, bufferPath],
outputCurve=xsdSubFile,
operation=XSDataString("SUB"))
self.lstSub.append("Merged data from : %s" %
self.dataInput.mergedCurve.path.value)
self.lstSub.append("Subtracted buffer: %s" %
bufferPath.path.value)
self.__edPluginExecDataop = self.loadPlugin(
self.__strControlledPluginDatop)
self.__edPluginExecDataop.setDataInput(xsdSub)
self.__edPluginExecDataop.connectSUCCESS(
self.doSuccessExecDatop)
self.__edPluginExecDataop.connectFAILURE(
self.doFailureExecDatop)
self.__edPluginExecDataop.executeSynchronous()
if self.isFailure():
return
elif self.strSubFile is not None:
self.__edPluginExecAutoRg = self.loadPlugin(
self.__strControlledPluginAutoRG)
xsd = XSDataInputAutoRg(inputCurve=[xsdSubFile])
self.__edPluginExecAutoRg.setDataInput(xsd)
self.__edPluginExecAutoRg.connectSUCCESS(
self.doSuccessExecAutoRg)
self.__edPluginExecAutoRg.connectFAILURE(
self.doFailureExecAutoRg)
self.__edPluginExecAutoRg.executeSynchronous()
self.rewriteHeader(self.strSubFile, self.strSubFile)
else:
self.__edPluginExecAutoRg = self.loadPlugin(
self.__strControlledPluginAutoRG)
xsd = XSDataInputAutoRg(
inputCurve=[self.dataInput.mergedCurve])
self.__edPluginExecAutoRg.setDataInput(xsd)
self.__edPluginExecAutoRg.connectSUCCESS(
self.doSuccessExecAutoRg)
self.__edPluginExecAutoRg.connectFAILURE(
self.doFailureExecAutoRg)
self.__edPluginExecAutoRg.executeSynchronous()
def testIsSameExperimentalCondition(self):
edPluginSubWedgeMergev1_1 = self.createPlugin()
xsDataExperimentalConditionReference = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionSameAsReference = self.getTestExperimentalCondition(
)
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionSameAsReference), True)
xsDataExperimentalConditionDifferentExposureTime = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentExposureTime.getBeam(
).setExposureTime(XSDataTime(10.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentExposureTime), False)
xsDataExperimentalConditionDifferentWavelength = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentWavelength.getBeam().setWavelength(
XSDataWavelength(1.5))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentWavelength), False)
xsDataExperimentalConditionDifferentBeamPositionX = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentBeamPositionX.getDetector(
).setBeamPositionX(XSDataLength(20.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentBeamPositionX), False)
xsDataExperimentalConditionDifferentBeamPositionY = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentBeamPositionY.getDetector(
).setBeamPositionY(XSDataLength(20.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentBeamPositionY), False)
xsDataExperimentalConditionDifferentDistance = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentDistance.getDetector().setDistance(
XSDataLength(220.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentDistance), False)
xsDataExperimentalConditionDifferentName = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentName.getDetector().setName(
XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentName), False)
xsDataExperimentalConditionDifferentNumberPixelX = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentNumberPixelX.getDetector(
).setNumberPixelX(XSDataInteger(2))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentNumberPixelX), False)
xsDataExperimentalConditionDifferentNumberPixelY = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentNumberPixelY.getDetector(
).setNumberPixelY(XSDataInteger(2))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentNumberPixelY), False)
xsDataExperimentalConditionDifferentSerialNumber = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentSerialNumber.getDetector(
).setSerialNumber(XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentSerialNumber), False)
xsDataExperimentalConditionDifferentTwoTheta = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentTwoTheta.getDetector().setTwoTheta(
XSDataAngle(90.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentTwoTheta), False)
xsDataExperimentalConditionDifferentOscillationWidth = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentOscillationWidth.getGoniostat(
).setOscillationWidth(XSDataAngle(2.0))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentOscillationWidth), False)
xsDataExperimentalConditionDifferentRotationAxis = self.getTestExperimentalCondition(
)
xsDataExperimentalConditionDifferentRotationAxis.getGoniostat(
).setRotationAxis(XSDataString(u"EDNA"))
EDAssert.equal(
edPluginSubWedgeMergev1_1.isSameExperimentalCondition(
xsDataExperimentalConditionReference,
xsDataExperimentalConditionDifferentRotationAxis), False)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'title':
obj_ = XSDataString()
obj_.build(child_)
self.setTitle(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataQ':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataQ.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataQArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataQArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataValues':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataValues.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataIArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataIArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataStdDev':
obj_ = XSDataDouble()
obj_.build(child_)
self.experimentalDataStdDev.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataStdArray':
obj_ = XSDataArray()
obj_.build(child_)
self.setExperimentalDataStdArray(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalDataFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setExperimentalDataFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'rMaxSearchSettings':
obj_ = XSDataSolutionScatteringSettings()
obj_.build(child_)
self.setRMaxSearchSettings(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'angularUnits':
obj_ = XSDataInteger()
obj_.build(child_)
self.setAngularUnits(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'symmetry':
obj_ = XSDataString()
obj_.build(child_)
self.setSymmetry(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mode':
obj_ = XSDataString()
obj_.build(child_)
self.setMode(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'iNbThreads':
obj_ = XSDataInteger()
obj_.build(child_)
self.setINbThreads(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'onlyGnom':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setOnlyGnom(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'plotFit':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setPlotFit(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'qMin':
obj_ = XSDataDouble()
obj_.build(child_)
self.setQMin(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'qMax':
obj_ = XSDataDouble()
obj_.build(child_)
self.setQMax(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataCollectionId':
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dirN':
obj_ = XSDataFile()
obj_.build(child_)
self.setDirN(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'templateN':
obj_ = XSDataString()
obj_.build(child_)
self.setTemplateN(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'fromN':
obj_ = XSDataInteger()
obj_.build(child_)
self.setFromN(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'toN':
obj_ = XSDataInteger()
obj_.build(child_)
self.setToN(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'processDirectory':
obj_ = XSDataFile()
obj_.build(child_)
self.setProcessDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'doAnomAndNonanom':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setDoAnomAndNonanom(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def getXSDataXDSDetector(_xsDataDetector):
EDFactoryPluginStatic.loadModule("XSDataXDSv1_0")
from XSDataXDSv1_0 import XSDataXDSDetector
from XSDataXDSv1_0 import XSDataXDSIntegerRange
xsDataXDSDetector = XSDataXDSDetector()
strDetectorType = _xsDataDetector.getType().getValue()
if ((strDetectorType == "q4") or \
(strDetectorType == "q4-2x") or \
(strDetectorType == "q210") or \
(strDetectorType == "q210-2x") or \
(strDetectorType == "q315") or \
(strDetectorType == "q315-2x")):
xsDataXDSDetector.setDetector_name(XSDataString("ADSC"))
xsDataXDSDetector.setMinimum_valid_pixel_value(XSDataInteger(1))
xsDataXDSDetector.setOverload(XSDataInteger(65535))
xsDataXDSIntegerRangeTrustedPixel = XSDataXDSIntegerRange()
xsDataXDSIntegerRangeTrustedPixel.setLower(XSDataInteger(6000))
xsDataXDSIntegerRangeTrustedPixel.setUpper(XSDataInteger(30000))
xsDataXDSDetector.setValue_range_for_trusted_detector_pixels(
xsDataXDSIntegerRangeTrustedPixel)
# elif ( strDetectorType == "mar165") or \
# strDetectorType == "mar225") ):
# xsDataXDSDetector.setType( XSDataString( "MARCCD" ) )
elif strDetectorType == "pilatus6m":
xsDataXDSDetector.setDetector_name(XSDataString("PILATUS"))
listUntrustedRectangle = \
[[ 487, 495, 0, 2528], \
[ 981, 989, 0, 2528], \
[1475, 1483, 0, 2528], \
[1969, 1977, 0, 2528], \
[ 0, 2464, 195, 213], \
[ 0, 2464, 407, 425], \
[ 0, 2464, 619, 637], \
[ 0, 2464, 831, 849], \
[ 0, 2464, 1043, 1061], \
[ 0, 2464, 1255, 1273], \
[ 0, 2464, 1467, 1485], \
[ 0, 2464, 1679, 1697], \
[ 0, 2464, 1891, 1909], \
[ 0, 2464, 2103, 2121], \
[ 0, 2464, 2315, 2333]]
for listRectangle in listUntrustedRectangle:
xsDataXDSRectangle = XSDataXDSRectangle()
xsDataXDSRectangle.setX1(XSDataInteger(listRectangle[0]))
xsDataXDSRectangle.setX2(XSDataInteger(listRectangle[1]))
xsDataXDSRectangle.setY1(XSDataInteger(listRectangle[2]))
xsDataXDSRectangle.setY2(XSDataInteger(listRectangle[3]))
xsDataXDSDetector.addUntrusted_rectangle(xsDataXDSRectangle)
xsDataXDSDetector.setMinimum_valid_pixel_value(XSDataInteger(0))
xsDataXDSDetector.setOverload(XSDataInteger(1048500))
xsDataXDSIntegerRangeTrustedPixel = XSDataXDSIntegerRange()
xsDataXDSIntegerRangeTrustedPixel.setLower(XSDataInteger(7000))
xsDataXDSIntegerRangeTrustedPixel.setUpper(XSDataInteger(30000))
xsDataXDSDetector.setValue_range_for_trusted_detector_pixels(
xsDataXDSIntegerRangeTrustedPixel)
xsDataXDSDoubleRangeTrustedRegion = XSDataXDSDoubleRange()
xsDataXDSDoubleRangeTrustedRegion.setLower(XSDataDouble(0.0))
xsDataXDSDoubleRangeTrustedRegion.setUpper(XSDataDouble(1.41))
xsDataXDSDetector.setTrusted_region(
xsDataXDSDoubleRangeTrustedRegion)
xsDataXDSDetector.setSensor_thickness(XSDataDouble(0.32))
else:
# This is a temporary solution for the exception problem pointed out in bug #43.
# Instead of raising an exception with a known type we send the error message as a string.
pyStrErrorMessage = "EDHandlerXSDataXDSv1_0.getXSDataXDSDetector: Unknown detector type : " + strDetectorType
raise Exception, pyStrErrorMessage
xsDataXDSDetector.setNx(_xsDataDetector.getNumberPixelX())
xsDataXDSDetector.setNy(_xsDataDetector.getNumberPixelY())
xsDataXDSDetector.setQx(_xsDataDetector.getPixelSizeX())
xsDataXDSDetector.setQy(_xsDataDetector.getPixelSizeY())
xsDataXDSDetector.setDetector_distance(_xsDataDetector.getDistance())
fOrgx = _xsDataDetector.getBeamPositionY().getValue(
) / _xsDataDetector.getPixelSizeY().getValue()
fOrgy = _xsDataDetector.getBeamPositionX().getValue(
) / _xsDataDetector.getPixelSizeX().getValue()
xsDataXDSDetector.setOrgx(XSDataDouble(fOrgx))
xsDataXDSDetector.setOrgy(XSDataDouble(fOrgy))
xsDataVectorDoubleXAxis = XSDataVectorDouble()
xsDataVectorDoubleXAxis.setV1(1.0)
xsDataVectorDoubleXAxis.setV2(0.0)
xsDataVectorDoubleXAxis.setV3(0.0)
xsDataXDSDetector.setDirection_of_detector_x_axis(
xsDataVectorDoubleXAxis)
xsDataVectorDoubleYAxis = XSDataVectorDouble()
xsDataVectorDoubleYAxis.setV1(0.0)
xsDataVectorDoubleYAxis.setV2(1.0)
xsDataVectorDoubleYAxis.setV3(0.0)
xsDataXDSDetector.setDirection_of_detector_y_axis(
xsDataVectorDoubleYAxis)
return xsDataXDSDetector
def finallyProcess(self, _edObject=None):
EDPluginExec.finallyProcess(self)
self.DEBUG(
"EDPluginISPyBUpdateDataCollectionGroupWorkflowIdv1_4.finallyProcess"
)
xsDataResultISPyBUpdateDataCollectionGroupWorkflowId = XSDataResultISPyBUpdateDataCollectionGroupWorkflowId(
)
if self.iDataCollectionGroupId is not None:
xsDataResultISPyBUpdateDataCollectionGroupWorkflowId.dataCollectionGroupId = XSDataInteger(
self.iDataCollectionGroupId)
self.setDataOutput(
xsDataResultISPyBUpdateDataCollectionGroupWorkflowId)
def generateXSDataInputXDS(_xsDataCollection):
xsDataCollection = _xsDataCollection
xsDataExperimentalCondition = _xsDataCollection.getSubWedge(
)[0].getExperimentalCondition()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataInputXDS = XSDataInputXDSGenerateBackgroundImage()
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()
# Start with the detector
xsDataXDSDetector = EDHandlerXSDataXDSv1_0.getXSDataXDSDetector(
xsDataDetector)
xsDataInputXDS.setDetector(xsDataXDSDetector)
# Then the beam
xsDataXDSBeam = XSDataXDSBeam()
xsDataVectorDoubleIncidentBeam = XSDataVectorDouble()
xsDataVectorDoubleIncidentBeam.setV1(0.0)
xsDataVectorDoubleIncidentBeam.setV2(0.0)
xsDataVectorDoubleIncidentBeam.setV3(1.0)
xsDataXDSBeam.setIncident_beam_direction(
xsDataVectorDoubleIncidentBeam)
xsDataVectorDoublePolarizationPlaneNormal = XSDataVectorDouble()
xsDataVectorDoublePolarizationPlaneNormal.setV1(0.0)
xsDataVectorDoublePolarizationPlaneNormal.setV2(1.0)
xsDataVectorDoublePolarizationPlaneNormal.setV3(0.0)
xsDataXDSBeam.setPolarization_plane_normal(
xsDataVectorDoublePolarizationPlaneNormal)
xsDataXDSBeam.setX_ray_wavelength(XSDataWavelength(dWavelength))
xsDataInputXDS.setBeam(xsDataXDSBeam)
# Then the goniostat
xsDataXDSGoniostat = XSDataXDSGoniostat()
xsDataVectorDoubleRotationAxis = XSDataVectorDouble()
xsDataVectorDoubleRotationAxis.setV1(1.0)
xsDataVectorDoubleRotationAxis.setV2(0.0)
xsDataVectorDoubleRotationAxis.setV3(0.0)
xsDataXDSGoniostat.setRotation_axis(xsDataVectorDoubleRotationAxis)
xsDataXDSGoniostat.setOscillation_range(
xsDataGoniostat.getOscillationWidth())
xsDataXDSGoniostat.setStarting_angle(
xsDataGoniostat.getRotationAxisStart())
xsDataInputXDS.setGoniostat(xsDataXDSGoniostat)
# # Then the Crystal
#
# xsDataXDSCrystal = XSDataXDSCrystal()
#
# xsDataXDSCrystal.setFriedels_law(XSDataString("FALSE"))
#
## if ( xsDataCrystal is not None ):
## xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
## if ( xsDataSpaceGroup is not None ):
## xsDataStringName = xsDataSpaceGroup.getName()
## if ( xsDataStringName is not None ):
## xsDataInputXDS.setSymmetry( XSDataString( xsDataStringName.getValue() ) )
# xsDataXDSCrystal.setSpace_group_number(XSDataInteger(0))
#
# xsDataXDSCrystal.setStrong_pixel(XSDataInteger(8))
#
# xsDataCell = XSDataCell()
# xsDataCell.setLength_a(XSDataLength(0.0))
# xsDataCell.setLength_b(XSDataLength(0.0))
# xsDataCell.setLength_c(XSDataLength(0.0))
# xsDataCell.setAngle_alpha(XSDataAngle(0.0))
# xsDataCell.setAngle_beta(XSDataAngle(0.0))
# xsDataCell.setAngle_gamma(XSDataAngle(0.0))
# xsDataXDSCrystal.setUnit_cell_constants(xsDataCell)
#
# xsDataInputXDS.setCrystal(xsDataXDSCrystal)
# Finaly the images
xsDataXDSImage = XSDataXDSImage()
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
pyStrPath = xsDataImageFirst.getPath().getValue()
pyStrFileName = EDUtilsFile.getBaseName(pyStrPath)
pyStrDirectory = EDUtilsPath.getFolderName(pyStrPath)
pyStrPrefix = EDUtilsImage.getPrefix(pyStrFileName)
pyStrSuffix = EDUtilsImage.getSuffix(pyStrFileName)
pyStrXDSTemplate = "%s_xdslink_?????.%s" % (pyStrPrefix, pyStrSuffix)
xsDataXDSImage.setName_template_of_data_frames(
XSDataString(pyStrXDSTemplate))
iXDSLowestImageNumberGlobal = 1
xsDataXDSImage.setStarting_frame(
XSDataInteger(iXDSLowestImageNumberGlobal))
# First we have to find the smallest goniostat rotation axis start:
fGonioStatOscillationStartMin = None
for xsDataSubWedge in xsDataSubWedgeList:
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
if (fGonioStatOscillationStartMin is None):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
elif (fGonioStatOscillationStartMin > fGonioStatOscillationStart):
fGonioStatOscillationStartMin = fGonioStatOscillationStart
# 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 and highest image numbers
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
iLowestXDSImageNumber = None
iHighestXDSImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
fImageOscillationStart = fGonioStatOscillationStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
iXDSImageNumber = iXDSLowestImageNumberGlobal + int(
(fImageOscillationStart - fGonioStatOscillationStartMin) /
fGonioStatOscillationRange)
#print iXDSImageNumber, fImageOscillationStart, fGonioStatOscillationStartMin, fGonioStatOscillationRange
pyStrSourcePath = xsDataImage.getPath()
pyStrTarget = "%s_xdslink_%05d.%s" % (
pyStrPrefix, iXDSImageNumber, pyStrSuffix)
xsDataXDSImageLink = XSDataXDSImageLink()
xsDataFileSource = XSDataFile()
xsDataFileSource.setPath(pyStrSourcePath)
xsDataXDSImageLink.setSource(xsDataFileSource)
xsDataXDSImageLink.setTarget(XSDataString(pyStrTarget))
xsDataInputXDS.addImage_link(xsDataXDSImageLink)
if (iLowestXDSImageNumber is None):
iLowestXDSImageNumber = iXDSImageNumber
elif (iLowestXDSImageNumber > iXDSImageNumber):
iLowestXDSImageNumber = iXDSImageNumber
if (iHighestXDSImageNumber is None):
iHighestXDSImageNumber = iXDSImageNumber
elif (iHighestXDSImageNumber < iXDSImageNumber):
iHighestXDSImageNumber = iXDSImageNumber
xsDataXDSIntegerRange = XSDataXDSIntegerRange()
xsDataXDSIntegerRange.setLower(
XSDataInteger(iLowestXDSImageNumber))
xsDataXDSIntegerRange.setUpper(
XSDataInteger(iHighestXDSImageNumber))
xsDataXDSImage.addBackground_range(xsDataXDSIntegerRange)
xsDataXDSImage.addData_range(xsDataXDSIntegerRange)
xsDataXDSImage.addSpot_range(xsDataXDSIntegerRange)
xsDataInputXDS.setImage(xsDataXDSImage)
return xsDataInputXDS
"Usage: id29_create_thumbnail image_directory_path image1 [image2]"
)
sys.exit(1)
EDVerbose.screen("Arguments: %r" % sys.argv)
strPathToTempDir = tempfile.mkdtemp(prefix="id29_create_thumbnail_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(
os.path.join(strPathToTempDir, "id29_create_thumbnail.log"))
strImageDirectory = sys.argv[1]
listImageName = sys.argv[2:]
# Quick check if the two image names are the same. If they are launch the thumbnail generator only once
if len(listImageName) == 2:
if listImageName[0] == listImageName[1]:
listImageName = [listImageName[0]]
for strImageName in listImageName:
xsDataInputPyarchThumbnailGenerator = XSDataInputPyarchThumbnailGenerator(
)
xsDataInputPyarchThumbnailGenerator.setWaitForFileTimeOut(
XSDataInteger(1000))
strImagePath = os.path.join(strImageDirectory, strImageName)
xsDataInputPyarchThumbnailGenerator.setDiffractionImage(
XSDataFile(XSDataString(strImagePath)))
EDVerbose.screen(
"XML input for EDPluginControlPyarchThumbnailGeneratorv1_0: %s" %
xsDataInputPyarchThumbnailGenerator.marshal())
edPluginControlPyarchThumbnailGeneratorv1_0 = EDPluginControlPyarchThumbnailGeneratorv1_0(
)
edPluginControlPyarchThumbnailGeneratorv1_0.setDataInput(
xsDataInputPyarchThumbnailGenerator)
edPluginControlPyarchThumbnailGeneratorv1_0.execute()
def setPluginInput(self, _edPlugin):
xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not self.__fMaxExposureTimePerDataCollection is None):
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(self.__fMaxExposureTimePerDataCollection))
if (not self.__strForcedSpaceGroup is None):
xsDataDiffractionPlan.setForcedSpaceGroup(
XSDataString(self.__strForcedSpaceGroup))
if (not self.__bAnomalousData is None):
xsDataDiffractionPlan.setAnomalousData(
XSDataBoolean(self.__bAnomalousData))
if (not self.__strStrategyOption is None):
xsDataDiffractionPlan.setStrategyOption(
XSDataString(self.__strStrategyOption))
if (not self.__fDoseLimit is None):
xsDataDiffractionPlan.setDoseLimit(XSDataDouble(self.__fDoseLimit))
if (not self.__fAimedCompleteness is None):
xsDataDiffractionPlan.setAimedCompleteness(
XSDataDouble(self.__fAimedCompleteness))
if (not self.__fAimedMultiplicity is None):
xsDataDiffractionPlan.setAimedMultiplicity(
XSDataDouble(self.__fAimedMultiplicity))
if (not self.__fAimedResolution is None):
xsDataDiffractionPlan.setAimedResolution(
XSDataDouble(self.__fAimedResolution))
if (not self.__strComplexity is None):
xsDataDiffractionPlan.setComplexity(
XSDataString(self.__strComplexity))
_edPlugin.setDataInput(xsDataDiffractionPlan, "diffractionPlan")
if (not self.__listImagePaths is None):
for strImagePath in self.__listImagePaths:
_edPlugin.setDataInput(XSDataString(strImagePath),
"imagePaths")
if (not self.__xsDataInputCharacterisation is None):
_edPlugin.setDataInput(self.__xsDataInputCharacterisation,
"inputCharacterisation")
if (not self.__fFlux is None):
_edPlugin.setDataInput(XSDataFloat(self.__fFlux), "flux")
if (not self.__fMinExposureTimePerImage is None):
_edPlugin.setDataInput(
XSDataFloat(self.__fMinExposureTimePerImage),
"minExposureTimePerImage")
if (not self.__fBeamSize is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamSize), "beamSize")
if (not self.__bTemplateMode is None):
_edPlugin.setDataInput(XSDataBoolean(self.__bTemplateMode),
"templateMode")
if (not self.__strGeneratedTemplateFile is None):
_edPlugin.setDataInput(
XSDataString(self.__strGeneratedTemplateFile),
"generatedTemplateFile")
if (not self.__strResultsFilePath is None):
_edPlugin.setDataInput(XSDataString(self.__strResultsFilePath),
"resultsFilePath")
if (not self.__fBeamPosX is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamPosX), "beamPosX")
if (not self.__fBeamPosY is None):
_edPlugin.setDataInput(XSDataFloat(self.__fBeamPosY), "beamPosY")
if (not self.__iDataCollectionId is None):
_edPlugin.setDataInput(XSDataInteger(self.__iDataCollectionId),
"dataCollectionId")
if (not self.__strShortComments is None):
_edPlugin.setDataInput(XSDataString(self.__strShortComments),
"shortComments")
if (not self.__strComments is None):
_edPlugin.setDataInput(XSDataString(self.__strComments),
"comments")
if (not self.__fTransmission is None):
_edPlugin.setDataInput(XSDataDouble(self.__fTransmission),
"transmission")
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 process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlXDSAPPv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
if self.dataInput.startImageNumber is not None:
imageNoStart = self.dataInput.startImageNumber.value
if self.dataInput.endImageNumber is not None:
imageNoEnd = self.dataInput.endImageNumber.value
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
if imageNoStart is None:
imageNoStart = ispybDataCollection.startImageNumber
if imageNoEnd is None:
imageNoEnd = ispybDataCollection.startImageNumber + \
ispybDataCollection.numberOfImages - 1
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(
directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(
directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.value
template = self.dataInput.templateN.value
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory,
fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
# Create path to pyarch
if self.dataInput.reprocess is not None and self.dataInput.reprocess.value:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchReprocessDirectoryPath(
beamline, "XDSAPP", self.dataInput.dataCollectionId.value)
else:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
self.resultsDirectory)
self.pyarchDirectory = self.pyarchDirectory.replace(
'PROCESSED_DATA', 'RAW_DATA')
if self.pyarchDirectory is not None and not os.path.exists(
self.pyarchDirectory):
try:
os.makedirs(self.pyarchDirectory, 0o755)
except:
self.pyarchDirectory = None
# Determine pyarch prefix
listPrefix = template.split("_")
self.pyarchPrefix = "xa_{0}_run{1}".format(listPrefix[-3],
listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage
for beamline in ["id23eh1", "id29"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage
for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(
directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(
directory, self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(
XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (
fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(
XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (
fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
if self.dataInput.hdf5ToCbfDirectory is not None:
dir = self.dataInput.hdf5ToCbfDirectory.path.value
pathToStartImage = glob.glob(os.path.join(dir, "*000001*"))[0]
self.timeStart = time.localtime()
# Prepare input to execution plugin
if self.doAnom:
xsDataInputXDSAPPAnom = XSDataInputXDSAPP()
xsDataInputXDSAPPAnom.startImageNumber = self.dataInput.startImageNumber
xsDataInputXDSAPPAnom.endImageNumber = self.dataInput.endImageNumber
xsDataInputXDSAPPAnom.anomalous = XSDataBoolean(True)
xsDataInputXDSAPPAnom.image = XSDataFile(
XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPAnom.spacegroup = XSDataString(
self.xdsAppSpacegroup)
self.edPluginExecXDSAPPAnom.dataInput = xsDataInputXDSAPPAnom
self.edPluginExecXDSAPPAnom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=True,
timeStart=self.timeStart)
if self.doNoanom:
xsDataInputXDSAPPNoanom = XSDataInputXDSAPP()
xsDataInputXDSAPPNoanom.startImageNumber = self.dataInput.startImageNumber
xsDataInputXDSAPPNoanom.endImageNumber = self.dataInput.endImageNumber
xsDataInputXDSAPPNoanom.anomalous = XSDataBoolean(False)
xsDataInputXDSAPPNoanom.image = XSDataFile(
XSDataString(pathToStartImage))
if self.xdsAppSpacegroup is not None:
xsDataInputXDSAPPNoanom.spacegroup = XSDataString(
self.xdsAppSpacegroup)
self.edPluginExecXDSAPPNoanom.dataInput = xsDataInputXDSAPPNoanom
self.edPluginExecXDSAPPNoanom.execute()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to started
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingPrograms=self.processingPrograms, isAnom=False,
timeStart=self.timeStart)
if self.doAnom:
self.edPluginExecXDSAPPAnom.synchronize()
xsDataResultXDSAPPAnom = self.edPluginExecXDSAPPAnom.dataOutput
# Run XSCALE even if XSCALE.LP is present
strPathXscaleLpAnom = self.runXscale(
self.edPluginExecXDSAPPAnom.getWorkingDirectory(),
anom=True,
merged=True)
if self.doNoanom:
self.edPluginExecXDSAPPNoanom.synchronize()
xsDataResultXDSAPPNoanom = self.edPluginExecXDSAPPNoanom.dataOutput
strPathXscaleLpNoanom = self.runXscale(
self.edPluginExecXDSAPPNoanom.getWorkingDirectory(),
anom=False,
merged=True)
self.timeEnd = time.localtime()
# Upload to ISPyB
if self.dataInput.dataCollectionId is not None:
# Check if we should use XDS_ASCII_to_XML.pl
if self.doAnom:
if self.useXdsAsciiToXml:
# Only for anom runs
self.runXdsAsciiToXml(
xsDataResultXDSAPPAnom,
self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom,
self.autoProcProgramIdAnom)
else:
self.hasUploadedAnomResultsToISPyB = self.uploadToISPyB(
xsDataResultXDSAPPAnom, processDirectory, template,
strPathXscaleLpAnom, True, proposal, self.timeStart,
self.timeEnd, self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdAnom,
self.autoProcProgramIdAnom)
if self.hasUploadedAnomResultsToISPyB:
self.screen("Anom results uploaded to ISPyB")
else:
self.ERROR("Could not upload anom results to ISPyB!")
if self.doNoanom:
self.hasUploadedNoanomResultsToISPyB = self.uploadToISPyB(
xsDataResultXDSAPPNoanom, processDirectory, template,
strPathXscaleLpNoanom, False, proposal, self.timeStart,
self.timeEnd, self.dataInput.dataCollectionId.value,
self.autoProcIntegrationIdNoanom,
self.autoProcProgramIdNoanom)
if self.hasUploadedNoanomResultsToISPyB:
self.screen("Noanom results uploaded to ISPyB")
else:
self.ERROR("Could not upload noanom results to ISPyB!")
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlSaxsModelingv1_1.process")
xsDataInputDammif = XSDataInputDammif(gnomOutputFile=self.xsGnomFile,
unit=XSDataString(self.unit),
symmetry=XSDataString(
self.symmetry),
mode=XSDataString(self.mode))
for i in range(self.dammif_jobs):
dammif = self.loadPlugin(self.strPluginExecDammif)
dammif.connectSUCCESS(self.doSuccessExecDammif)
dammif.connectFAILURE(self.doFailureExecDammif)
xsd = xsDataInputDammif.copyViaDict()
xsd.order = XSDataInteger(i + 1)
dammif.dataInput = xsd
self.addPluginToActionCluster(dammif)
self.dammif_plugins.append(dammif)
self.executeActionCluster()
self.synchronizeActionCluster()
for plugin in self.dammif_plugins:
if plugin.isFailure():
self.ERROR("dammif plugin %s-%08i failed" %
(plugin.getName(), plugin.getId()))
self.setFailure()
self.retrieveMessages(plugin)
if self.isFailure():
return
# retrieve results from best dammif
self.dammif = self.bestDammif()
self.chi2plot("chi2_R.png")
self.result.chiRfactorPlot = XSDataFile(
XSDataString(os.path.join(self.getWorkingDirectory(),
"chi2_R.png")))
# temporary results: use best dammif
self.result.fitFile = self.dammif.dataOutput.fitFile
self.result.logFile = self.dammif.dataOutput.logFile
self.result.pdbMoleculeFile = self.dammif.dataOutput.pdbMoleculeFile
self.result.pdbSolventFile = self.dammif.dataOutput.pdbSolventFile
# align models, compute NSD and choose the reference model
inputfiles = [
self.dammif_plugins[idx].dataOutput.pdbMoleculeFile.path.value
for idx in range(self.dammif_jobs)
]
align = AlignModels(inputfiles, slow=False)
outputfiles = []
for i in range(self.dammif_jobs):
outputfiles.append(
os.path.join(self.getWorkingDirectory(),
"model-%02i.pdb" % (i + 1)))
align.outputfiles = outputfiles
#align.outputfiles = ["model-%02i.pdb" % (i+1) for i in range(self.dammif_jobs)]
align.validmodels = self.valid
align.assign_models()
align.makeNSDarray()
align.alignment_reference()
self.ref = align.reference
pngfile = os.path.join(self.getWorkingDirectory(), "nsd.png")
align.plotNSDarray(filename=pngfile, save=True)
self.result.nsdPlot = XSDataFile(XSDataString(pngfile))
# Now that all (valid) models are aligned we can combine them using damaver
pdbFiles = [XSDataFile(XSDataString(align.outputfiles[self.ref]))]
for idx in range(self.dammif_jobs):
if self.valid[idx] and idx != self.ref:
pdbFiles.append(
XSDataFile(XSDataString(align.outputfiles[idx])))
damaver = self.loadPlugin(self.strPluginExecDamaver)
damaver.dataInput = XSDataInputDamaver(pdbInputFiles=pdbFiles,
automatic=XSDataBoolean(False))
damaver.connectSUCCESS(self.doSuccessExecDamaver)
damaver.connectFAILURE(self.doFailureExecDamaver)
damaver.executeSynchronous()
if self.isFailure():
return
damfilt = self.loadPlugin(self.strPluginExecDamfilt)
damfilt.dataInput = XSDataInputDamfilt(
inputPdbFile=damaver.dataOutput.damaverPdbFile)
damfilt.connectSUCCESS(self.doSuccessExecDamfilt)
damfilt.connectFAILURE(self.doFailureExecDamfilt)
damfilt.execute()
########################################################################
# TODO: This is a dead end : do it in parallel
########################################################################
if self.isFailure():
return
damstart = self.loadPlugin(self.strPluginExecDamstart)
damstart.dataInput = XSDataInputDamstart(
inputPdbFile=damaver.dataOutput.damaverPdbFile)
damstart.connectSUCCESS(self.doSuccessExecDamstart)
damstart.connectFAILURE(self.doFailureExecDamstart)
damstart.executeSynchronous()
if self.isFailure():
return
########################################################################
# Finally call dammin
########################################################################
if self.config.get("do_dammin") in ["False", "0", False, 0]:
pass
#return
dammin = self.loadPlugin(self.strPluginExecDammin)
dammin.dataInput = XSDataInputDammin(
pdbInputFile=damstart.dataOutput.outputPdbFile,
gnomOutputFile=self.xsGnomFile,
symmetry=XSDataString(self.symmetry),
mode=XSDataString(self.mode))
dammin.connectSUCCESS(self.doSuccessExecDammin)
dammin.connectFAILURE(self.doFailureExecDammin)
dammin.executeSynchronous()
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hdf5ImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setHdf5ImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hdf5File':
obj_ = XSDataFile()
obj_.build(child_)
self.setHdf5File(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'forcedOutputDirectory':
obj_ = XSDataFile()
obj_.build(child_)
self.setForcedOutputDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'forcedOutputImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setForcedOutputImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'startImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setStartImageNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'endImageNumber':
obj_ = XSDataInteger()
obj_.build(child_)
self.setEndImageNumber(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_5.process")
xsdwf = XSDataInputWaitMultiFile(timeOut=XSDataTime(30),
expectedSize=XSDataInteger(10000),
expectedFile=[XSDataFile(i.path) for i in self.lstInput])
self.__edPluginExecWaitFile.setDataInput(xsdwf)
self.__edPluginExecWaitFile.connectFAILURE(self.doFailureExecWait)
self.__edPluginExecWaitFile.connectSUCCESS(self.doSuccessExecWait)
self.__edPluginExecWaitFile.executeSynchronous()
if self.isFailure():
return
if len(self.lstInput) == 1:
inp = self.lstInput[0].path.value
dst = self.dataInput.mergedCurve.path.value
if not os.path.isdir(os.path.dirname(dst)):
self.error("Output directory for %s does not exist" % dst)
os.makedirs(os.path.dirname(dst))
if not os.path.exists(inp):
self.warning("Input %s does not (yet?) exist" % inp)
time.sleep(1.0)
shutil.copyfile(inp, dst)
self.lstSummary.append("Got only one frame ... nothing to merge !!!")
else:
self.lstMerged = []
if (self.absoluteFidelity is not None) or (self.relativeFidelity is not None):
if self.absoluteFidelity is not None :
for idx, oneFile in enumerate(self.lstInput[1:]):
self.DEBUG("Calculating similarity of 0 and %s" % idx)
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], oneFile])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (self.relativeFidelity is not None):
if (self.absoluteFidelity is None):
self.DEBUG("Calculating similarity of 0 and 1")
edPluginExecAbsoluteFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[0], self.lstInput[1] ])
edPluginExecAbsoluteFidelity.setDataInput(xsd)
edPluginExecAbsoluteFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecAbsoluteFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecAbsoluteFidelity.execute()
if (len(self.lstInput) > 2):
for idx, oneFile in enumerate(self.lstInput[2:]):
self.DEBUG("Calculating similarity of %s and %s" % (idx, idx + 1))
edPluginExecRelativeFidelity = self.loadPlugin(self.__strControlledPluginDatcmp)
xsd = XSDataInputDatcmp(inputCurve=[self.lstInput[idx + 1], oneFile])
edPluginExecRelativeFidelity.setDataInput(xsd)
edPluginExecRelativeFidelity.connectFAILURE(self.doFailureExecDatcmp)
edPluginExecRelativeFidelity.connectSUCCESS(self.doSuccessExecDatcmp)
edPluginExecRelativeFidelity.execute()
self.synchronizePlugins()
for idx, oneFile in enumerate(self.lstInput):
if idx == 0:
self.lstMerged.append(oneFile)
elif (self.absoluteFidelity is not None) and (self.relativeFidelity is not None):
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity) and (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.absoluteFidelity is not None) :
if (0, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (0, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(0, idx)] >= self.absoluteFidelity):
self.lstMerged.append(oneFile)
else:
break
elif (self.relativeFidelity is not None) :
if (idx - 1, idx) not in self.dictSimilarities:
self.ERROR("dict missing %i,%i: \n" % (idx - 1, idx) + "\n".join([ "%s: %s" % (key, self.dictSimilarities[key]) for key in self.dictSimilarities]))
self.resynchronize()
if (self.dictSimilarities[(idx - 1, idx)] >= self.relativeFidelity):
self.lstMerged.append(oneFile)
else:
break
else:
self.lstMerged.append(oneFile)
self.lstMerged.sort(cmp)
if len(self.lstMerged) != len(self.lstInput):
self.strRadiationDamage = "Radiation damage detected, merged %i curves" % len(self.lstMerged)
self.WARNING(self.strRadiationDamage)
self.lstSummary.append("WARNING: " + self.strRadiationDamage)
self.lstSummary.append("Merging files: " + " ".join([os.path.basename(i.path.value) for i in self.lstMerged]))
if len(self.lstMerged) == 1:
self.rewriteHeader(self.lstMerged[0].path.value, self.strMergedFile)
else:
self.__edPluginExecDataver = self.loadPlugin(self.__strControlledPluginDataver)
xsd = XSDataInputDataver(inputCurve=self.lstMerged)
# outputCurve=self.dataInput.mergedCurve,
self.__edPluginExecDataver.setDataInput(xsd)
self.__edPluginExecDataver.connectSUCCESS(self.doSuccessExecDataver)
self.__edPluginExecDataver.connectFAILURE(self.doFailureExecDataver)
self.__edPluginExecDataver.executeSynchronous()
if (self.fConcentration == 0) and (self.strSubFile is not None):
if (self.__class__.lastBuffer is not None) and (self.__class__.lastSample is not None):
self.__edPluginExecAutoSub = self.loadPlugin(self.__strControlledPluginAutoSub)
base = "_".join(os.path.basename(self.__class__.lastSample.path.value).split("_")[:-1])
suff = os.path.basename(self.strSubFile).split("_")[-1]
sub = os.path.join(os.path.dirname(self.strSubFile), base + "_" + suff)
xsdSubtractedCurve = XSDataFile(XSDataString(sub))
self.curves.append(xsdSubtractedCurve)
self.__edPluginExecAutoSub.dataInput = XSDataInputAutoSub(sampleCurve=self.__class__.lastSample,
buffers=[self.__class__.lastBuffer, self.dataInput.mergedCurve],
subtractedCurve=xsdSubtractedCurve)
self.__edPluginExecAutoSub.connectSUCCESS(self.doSuccessExecAutoSub)
self.__edPluginExecAutoSub.connectFAILURE(self.doFailureExecAutoSub)
self.__edPluginExecAutoSub.executeSynchronous()
if self.isFailure():
return
self.__edPluginSaxsAnalysis = self.loadPlugin(self.__strControlledPluginSaxsAnalysis)
self.__edPluginSaxsAnalysis.dataInput = XSDataInputSaxsAnalysis(scatterCurve=xsdSubtractedCurve,
autoRg=self.autoRg)
self.__edPluginSaxsAnalysis.connectSUCCESS(self.doSuccessSaxsAnalysis)
self.__edPluginSaxsAnalysis.connectFAILURE(self.doFailureSaxsAnalysis)
self.__edPluginSaxsAnalysis.executeSynchronous()
self.__class__.lastBuffer = self.dataInput.mergedCurve
self.__class__.lastSample = None
else:
self.__class__.lastSample = self.dataInput.mergedCurve
if self.dataInput.sample.login and self.dataInput.sample.passwd and self.dataInput.sample.measurementID:
self.lstSummary.append("Registering to ISPyB")
self.__edPluginSaxsISPyB = self.loadPlugin(self.__strControlledPluginSaxsISPyB)
if len(self.lstInput) > 1:
frameAverage = XSDataInteger(len(self.lstInput))
frameMerged = XSDataInteger(len(self.lstMerged))
else:
frameMerged = frameAverage = XSDataInteger(1)
self.curves = [XSDataFile(i.path) for i in self.lstInput]
if self.strMergedFile is not None:
self.curves.append(XSDataFile(XSDataString(self.strMergedFile)))
xsdin = XSDataInputBioSaxsISPyBv1_0(sample=self.dataInput.sample,
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.volume,
frameAverage=frameAverage,
frameMerged=frameMerged,
curves=self.curves,
bestBuffer=self.xsBestBuffer
# destination=self.dataInput.sample.ispybDestination #duplicate, already in sample
)
self.__edPluginSaxsISPyB.dataInput = xsdin
self.__edPluginSaxsISPyB.connectSUCCESS(self.doSuccessISPyB)
self.__edPluginSaxsISPyB.connectFAILURE(self.doFailureISPyB)
self.__edPluginSaxsISPyB.execute()
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_2.process")
EDUtilsParallel.initializeNbThread()
# Check if we should do indexing:
bDoIndexing = False
if self.dataInput.doIndexing is not None:
if self.dataInput.doIndexing.value:
bDoIndexing = True
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators(
)
listPlugin = []
for xsDataImage in listXSDataImage:
self.edPluginMXWaitFile = self.loadPlugin(
self.strPluginMXWaitFileName)
xsDataInputMXWaitFile.file = XSDataFile(xsDataImage.path)
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(
XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
self.edPluginMXWaitFile.executeSynchronous()
if not os.path.exists(xsDataImage.path.value):
strError = "Time-out while waiting for image %s" % xsDataImage.path.value
self.error(strError)
self.addErrorMessage(strError)
self.setFailure()
else:
if self.bUseThinClient:
strPluginName = self.strPluginNameThinClient
else:
strPluginName = self.strPluginName
edPluginPluginExecImageQualityIndicator = self.loadPlugin(
strPluginName)
listPlugin.append(edPluginPluginExecImageQualityIndicator)
self.listPluginExecImageQualityIndicator.append(
edPluginPluginExecImageQualityIndicator)
xsDataInputDistlSignalStrength = XSDataInputDistlSignalStrength(
)
xsDataInputDistlSignalStrength.setReferenceImage(xsDataImage)
edPluginPluginExecImageQualityIndicator.setDataInput(
xsDataInputDistlSignalStrength)
edPluginPluginExecImageQualityIndicator.execute()
listIndexing = []
# Synchronize all image quality indicator plugins and upload to ISPyB
xsDataInputStoreListOfImageQualityIndicators = XSDataInputStoreListOfImageQualityIndicators(
)
for edPluginPluginExecImageQualityIndicator in listPlugin:
edPluginPluginExecImageQualityIndicator.synchronize()
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString( \
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(
xsDataImageQualityIndicators)
xsDataISPyBImageQualityIndicators = \
XSDataISPyBImageQualityIndicators.parseString(xsDataImageQualityIndicators.marshal())
xsDataInputStoreListOfImageQualityIndicators.addImageQualityIndicators(
xsDataISPyBImageQualityIndicators)
# print xsDataInputStoreListOfImageQualityIndicators.marshal()
if self.bDoISPyBUpload:
self.edPluginISPyB = self.loadPlugin(self.strISPyBPluginName)
self.edPluginISPyB.dataInput = xsDataInputStoreListOfImageQualityIndicators
self.edPluginISPyB.execute()
#
if bDoIndexing:
# Find the 5 most intensive images (TIS):
listImage = []
listSorted = sorted(
self.xsDataResultControlImageQualityIndicators.
imageQualityIndicators,
key=lambda imageQualityIndicators: imageQualityIndicators.
totalIntegratedSignal.value)
for xsDataResultControlImageQualityIndicator in listSorted[-5:]:
if xsDataResultControlImageQualityIndicator.goodBraggCandidates.value > 30:
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(
xsDataResultControlImageQualityIndicator.image.path)
self.edPluginReadImageHeader = self.loadPlugin(
self.strPluginReadImageHeaderName)
self.edPluginReadImageHeader.dataInput = xsDataInputReadImageHeader
self.edPluginReadImageHeader.executeSynchronous()
xsDataResultReadImageHeader = self.edPluginReadImageHeader.dataOutput
if xsDataResultReadImageHeader is not None:
xsDataSubWedge = xsDataResultReadImageHeader.subWedge
self.xsDataCollection = XSDataCollection()
self.xsDataCollection.addSubWedge(xsDataSubWedge)
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(
self.xsDataCollection)
xsDataMOSFLMIndexingInput = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing(
xsDataIndexingInput)
edPluginMOSFLMIndexing = self.loadPlugin(
self.strIndexingMOSFLMPluginName)
self.listPluginMOSFLM.append([
edPluginMOSFLMIndexing,
xsDataResultControlImageQualityIndicator
])
edPluginMOSFLMIndexing.setDataInput(
xsDataMOSFLMIndexingInput)
edPluginMOSFLMIndexing.execute()
for tupleMOSFLM in self.listPluginMOSFLM:
edPluginMOSFLMIndexing = tupleMOSFLM[0]
xsDataResultControlImageQualityIndicator = tupleMOSFLM[1]
edPluginMOSFLMIndexing.synchronize()
if not edPluginMOSFLMIndexing.isFailure():
xsDataMOSFLMOutput = edPluginMOSFLMIndexing.dataOutput
xsDataIndexingResult = EDHandlerXSDataMOSFLMv10.generateXSDataIndexingResult(
xsDataMOSFLMOutput)
selectedSolution = xsDataIndexingResult.selectedSolution
if selectedSolution is not None:
xsDataResultControlImageQualityIndicator.selectedIndexingSolution = selectedSolution
def createDataMOSFLMOutputIndexing(self):
self.DEBUG("EDPluginMOSFLMIndexingv10.createDataMOSFLMOutputIndexing")
xsDataMOSFLMOutputIndexing = XSDataMOSFLMOutputIndexing()
# Read Newmat file
xsDataMOSFLMNewmat = self.getDataMOSFLMNewmat()
if (xsDataMOSFLMNewmat is None):
strError = "MOSFLM indexing error : No solution was obtained!"
self.ERROR(strError)
self.setFailure()
else:
xsDataMOSFLMOutputIndexing.setRefinedNewmat(xsDataMOSFLMNewmat)
# Then read the XML file
strDnaTablesXML = self.readProcessFile(self.getScriptBaseName() +
"_dnaTables.xml")
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
listXSTableMosaicityEstimation = EDUtilsTable.getTableListFromTables(
xsDataDnaTables, "mosaicity_estimation")
dMosaicityValueSum = 0.0
nValues = 0
for xsTableMosaicityEstimation in listXSTableMosaicityEstimation:
for xsListMosaicity in EDUtilsTable.getListsFromTable(
xsTableMosaicityEstimation, "mosaicity"):
dMosaicityValue = float(
EDUtilsTable.getItemFromList(xsListMosaicity,
"value").getValueOf_())
dMosaicityValueSum += dMosaicityValue
nValues += 1
xsDataFloatMosaicityEstimation = XSDataFloat()
xsDataFloatMosaicityEstimation.setValue(dMosaicityValueSum /
nValues)
xsDataMOSFLMOutputIndexing.setMosaicityEstimation(
xsDataFloatMosaicityEstimation)
xsTableRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "refinement")
if (xsTableRefinement is None):
strError = "MOSFLM indexing error : No solution was refined!"
self.ERROR(strError)
self.setFailure()
else:
xsListDeviations = EDUtilsTable.getListsFromTable(
xsTableRefinement, "deviations")[0]
dDeviationAngular = float(
EDUtilsTable.getItemFromList(xsListDeviations,
"angular").getValueOf_())
dDeviationPositional = float(
EDUtilsTable.getItemFromList(xsListDeviations,
"positional").getValueOf_())
xsDataMOSFLMOutputIndexing.setDeviationAngular(
XSDataAngle(dDeviationAngular))
xsDataMOSFLMOutputIndexing.setDeviationPositional(
XSDataLength(dDeviationPositional))
xsListResults = EDUtilsTable.getListsFromTable(
xsTableRefinement, "results")[0]
dDetectorDistance = float(
EDUtilsTable.getItemFromList(
xsListResults, "detector_distance").getValueOf_())
xsDataMOSFLMOutputIndexing.setRefinedDistance(
XSDataLength(dDetectorDistance))
xsListParameters = EDUtilsTable.getListsFromTable(
xsTableRefinement, "parameters")[0]
iSpotsUsed = int(
EDUtilsTable.getItemFromList(xsListParameters,
"used").getValueOf_())
iSpotsTotal = int(
EDUtilsTable.getItemFromList(xsListParameters,
"out_of").getValueOf_())
xsDataMOSFLMOutputIndexing.setSpotsUsed(
XSDataInteger(iSpotsUsed))
xsDataMOSFLMOutputIndexing.setSpotsTotal(
XSDataInteger(iSpotsTotal))
xsTableSolutionRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "solution_refinement")
xsListParameters = EDUtilsTable.getListsFromTable(
xsTableSolutionRefinement, "selection")[0]
iSelectedSolutionNumber = int(
EDUtilsTable.getItemFromList(xsListParameters,
"number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionNumber(
XSDataInteger(iSelectedSolutionNumber))
strSelectedSolutionSpaceGroup = (EDUtilsTable.getItemFromList(
xsListParameters, "spacegroup").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroup(
XSDataString(strSelectedSolutionSpaceGroup))
iSelectedSolutionSpaceGroupNumber = int(
EDUtilsTable.getItemFromList(
xsListParameters, "spacegroup_number").getValueOf_())
xsDataMOSFLMOutputIndexing.setSelectedSolutionSpaceGroupNumber(
XSDataInteger(iSelectedSolutionSpaceGroupNumber))
xsTableAutoIndexSolutions = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "autoindex_solutions")
xsListsSolution = xsTableAutoIndexSolutions.getList()
for xsListSolution in xsListsSolution:
xsDataMOSFLMIndexingSolution = XSDataMOSFLMIndexingSolution(
)
xsDataCell = XSDataCell()
iSolutionNumber = int(
EDUtilsTable.getItemFromList(xsListSolution,
"index").getValueOf_())
xsDataMOSFLMIndexingSolution.setIndex(
XSDataInteger(iSolutionNumber))
iPenalty = int(
EDUtilsTable.getItemFromList(xsListSolution,
"penalty").getValueOf_())
xsDataMOSFLMIndexingSolution.setPenalty(
XSDataInteger(iPenalty))
strLattice = (EDUtilsTable.getItemFromList(
xsListSolution, "lattice").getValueOf_())
xsDataMOSFLMIndexingSolution.setLattice(
XSDataString(strLattice))
dA = float(
EDUtilsTable.getItemFromList(xsListSolution,
"a").getValueOf_())
xsDataCell.setLength_a(XSDataLength(dA))
dB = float(
EDUtilsTable.getItemFromList(xsListSolution,
"b").getValueOf_())
xsDataCell.setLength_b(XSDataLength(dB))
dC = float(
EDUtilsTable.getItemFromList(xsListSolution,
"c").getValueOf_())
xsDataCell.setLength_c(XSDataLength(dC))
dAlpha = float(
EDUtilsTable.getItemFromList(xsListSolution,
"alpha").getValueOf_())
xsDataCell.setAngle_alpha(XSDataAngle(dAlpha))
dBeta = float(
EDUtilsTable.getItemFromList(xsListSolution,
"beta").getValueOf_())
xsDataCell.setAngle_beta(XSDataAngle(dBeta))
dGamma = float(
EDUtilsTable.getItemFromList(xsListSolution,
"gamma").getValueOf_())
xsDataCell.setAngle_gamma(XSDataAngle(dGamma))
xsDataMOSFLMIndexingSolution.setCell(xsDataCell)
xsDataMOSFLMOutputIndexing.addPossibleSolutions(
xsDataMOSFLMIndexingSolution)
xsTableBeamRefinement = EDUtilsTable.getTableFromTables(
xsDataDnaTables, "beam_refinement")
xsDataMOSFLMBeamPositionRefined = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPositionShift = XSDataMOSFLMBeamPosition()
dInitialBeamX = 0.0
dInitialBeamY = 0.0
dRefinedBeamX = 0.0
dRefinedBeamY = 0.0
xsListInitialBeam = EDUtilsTable.getListsFromTable(
xsTableBeamRefinement, "initial_beam")[0]
fInitialBeamPositionX = float(
EDUtilsTable.getItemFromList(xsListInitialBeam,
"x").getValueOf_())
fInitialBeamPositionY = float(
EDUtilsTable.getItemFromList(xsListInitialBeam,
"y").getValueOf_())
xsListRefinedBeam = EDUtilsTable.getListsFromTable(
xsTableBeamRefinement, "refined_beam")[0]
fRefinedBeamPositionX = float(
EDUtilsTable.getItemFromList(xsListRefinedBeam,
"x").getValueOf_())
fRefinedBeamPositionY = float(
EDUtilsTable.getItemFromList(xsListRefinedBeam,
"y").getValueOf_())
xsDataMOSFLMBeamPositionRefined.setX(
XSDataLength(fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionRefined.setY(
XSDataLength(fRefinedBeamPositionY))
xsDataMOSFLMBeamPositionShift.setX(
XSDataLength(fInitialBeamPositionX -
fRefinedBeamPositionX))
xsDataMOSFLMBeamPositionShift.setY(
XSDataLength(fInitialBeamPositionY -
fRefinedBeamPositionY))
xsDataMOSFLMOutputIndexing.setRefinedBeam(
xsDataMOSFLMBeamPositionRefined)
xsDataMOSFLMOutputIndexing.setBeamShift(
xsDataMOSFLMBeamPositionShift)
# Path to log file
xsDataMOSFLMOutputIndexing.setPathToLogFile(
XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName()))))
return xsDataMOSFLMOutputIndexing
def generateXSDataISPyBScreeningOutputContainer(
_xsDataResultCharacterisation, _strStatusMessage, _fKappa, _fPhi):
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.program = XSDataString("EDNA MXv1")
xsDataISPyBScreeningOutputLattice = None
# Indexing information
bSuccessfulIndexing = False
xsDataIndexingResult = _xsDataResultCharacterisation.getIndexingResult(
)
if (xsDataIndexingResult is not None):
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution(
)
if (xsDataIndexingSolutionSelected is not None):
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice(
)
bSuccessfulIndexing = True
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics(
)
if (xsDataStatisticsIndexing is not None):
xsDataISPyBScreeningOutput.beamShiftX = xsDataStatisticsIndexing.beamPositionShiftX
xsDataISPyBScreeningOutput.beamShiftY = xsDataStatisticsIndexing.beamPositionShiftY
xsDataISPyBScreeningOutput.spotDeviationR = xsDataStatisticsIndexing.spotDeviationPositional
xsDataISPyBScreeningOutput.spotDeviationTheta = xsDataStatisticsIndexing.spotDeviationAngular
if ((xsDataStatisticsIndexing.spotsTotal is not None) and
(xsDataStatisticsIndexing.spotsUsed is not None)):
iSpotsTotal = xsDataStatisticsIndexing.spotsTotal.value
iSpotsUsed = xsDataStatisticsIndexing.spotsUsed.value
xsDataISPyBScreeningOutput.numSpotsFound = xsDataStatisticsIndexing.spotsTotal
xsDataISPyBScreeningOutput.numSpotsUsed = xsDataStatisticsIndexing.spotsUsed
xsDataISPyBScreeningOutput.numSpotsRejected = XSDataInteger(
iSpotsTotal - iSpotsUsed)
xsDataCrystal = xsDataIndexingSolutionSelected.crystal
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(
False)
if (xsDataCrystal is not None):
if xsDataCrystal.mosaicity is not None:
xsDataISPyBScreeningOutput.mosaicity = xsDataCrystal.mosaicity
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(
True)
xsDataCell = xsDataCrystal.cell
if xsDataCell is not None:
xsDataISPyBScreeningOutputLattice.unitCell_a = xsDataCell.length_a
xsDataISPyBScreeningOutputLattice.unitCell_b = xsDataCell.length_b
xsDataISPyBScreeningOutputLattice.unitCell_c = xsDataCell.length_c
xsDataISPyBScreeningOutputLattice.unitCell_alpha = xsDataCell.angle_alpha
xsDataISPyBScreeningOutputLattice.unitCell_beta = xsDataCell.angle_beta
xsDataISPyBScreeningOutputLattice.unitCell_gamma = xsDataCell.angle_gamma
xsDataSpaceGroup = xsDataCrystal.spaceGroup
if xsDataSpaceGroup is not None:
xsDataISPyBScreeningOutputLattice.spaceGroup = xsDataSpaceGroup.name
if (bSuccessfulIndexing):
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(True))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing successful"))
else:
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(False))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing failed"))
# Strategy information
xsDataResultStrategy = _xsDataResultCharacterisation.strategyResult
xsDataISPyBScreeningStrategyContainer = None
xsDataISPyBScreeningStrategyWedgeContainer = None
if xsDataResultStrategy is None:
xsDataISPyBScreeningOutput.setStrategySuccess(XSDataBoolean(False))
else:
if xsDataResultStrategy.collectionPlan == []:
xsDataISPyBScreeningOutput.setStrategySuccess(
XSDataBoolean(False))
else:
xsDataISPyBScreeningOutput.setStrategySuccess(
XSDataBoolean(True))
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer(
)
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
listXSDataCollectionPlan = xsDataResultStrategy.collectionPlan
fTotalExposureTime = 0.0
iTotalNumberOfImages = 0
fTotalRotationRange = 0.0
for xsDataCollectionPlan in listXSDataCollectionPlan:
numberOfImagesWedge = None
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer(
)
xsDataISPyBScreeningStrategyWedge.wedgeNumber = xsDataCollectionPlan.collectionPlanNumber
fWavelength = _xsDataResultCharacterisation.dataCollection.subWedge[
0].experimentalCondition.beam.wavelength.value
xsDataISPyBScreeningStrategyWedge.wavelength = XSDataDouble(
fWavelength)
if _fKappa is not None:
xsDataISPyBScreeningStrategyWedge.kappa = XSDataDouble(
_fKappa)
if _fPhi is not None:
xsDataISPyBScreeningStrategyWedge.phi = XSDataDouble(
_fPhi)
if (xsDataCollectionPlan.getComment() is not None):
strCollectionPlanComment = xsDataCollectionPlan.getComment(
).getValue()
xsDataISPyBScreeningStrategyWedge.comments = strCollectionPlanComment
xsDataStrategySummary = xsDataCollectionPlan.strategySummary
if xsDataStrategySummary is not None:
xsDataISPyBScreeningStrategyWedge.completeness = xsDataStrategySummary.completeness
xsDataISPyBScreeningStrategyWedge.resolution = xsDataStrategySummary.resolution
xsDataISPyBScreeningStrategyWedge.multiplicity = xsDataStrategySummary.redundancy
xsDataISPyBScreeningOutput.rankingResolution = xsDataStrategySummary.rankingResolution
if xsDataStrategySummary.totalExposureTime is not None:
fTotalExposureTime += xsDataStrategySummary.totalExposureTime.value
xsDataCollectionStrategy = xsDataCollectionPlan.collectionStrategy
if xsDataCollectionStrategy is not None:
for xsDataSubWedge in xsDataCollectionStrategy.subWedge:
numberOfImagesSubWedge = None
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge(
)
xsDataISPyBScreeningStrategySubWedge.subWedgeNumber = xsDataSubWedge.subWedgeNumber
xsDataISPyBScreeningStrategySubWedge.axisStart = xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart
xsDataISPyBScreeningStrategySubWedge.axisEnd = xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd
xsDataISPyBScreeningStrategySubWedge.oscillationRange = xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth
# Number of images
if (xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart is not None) and \
(xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd is not None) and \
(xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth is not None):
numberOfImagesSubWedge = int((xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd.value - \
xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart.value) / \
xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth.value + 0.5)
xsDataISPyBScreeningStrategySubWedge.numberOfImages = XSDataInteger(
numberOfImagesSubWedge)
if numberOfImagesWedge is None:
numberOfImagesWedge = numberOfImagesSubWedge
else:
numberOfImagesWedge += numberOfImagesSubWedge
fTotalRotationRange += xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth.value * numberOfImagesSubWedge
xsDataISPyBScreeningStrategySubWedge.exposureTime = xsDataSubWedge.experimentalCondition.beam.exposureTime
xsDataISPyBScreeningStrategySubWedge.transmission = xsDataSubWedge.experimentalCondition.beam.transmission
xsDataISPyBScreeningStrategyWedgeContainer.addScreeningStrategySubWedge(
xsDataISPyBScreeningStrategySubWedge)
if numberOfImagesWedge is not None:
xsDataISPyBScreeningStrategyWedge.numberOfImages = XSDataInteger(
numberOfImagesWedge)
iTotalNumberOfImages += numberOfImagesWedge
xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategyWedge = xsDataISPyBScreeningStrategyWedge
xsDataISPyBScreeningStrategyContainer.addScreeningStrategyWedgeContainer(
xsDataISPyBScreeningStrategyWedgeContainer)
xsDataISPyBScreeningOutput.totalExposureTime = XSDataDouble(
fTotalExposureTime)
xsDataISPyBScreeningOutput.totalNumberOfImages = XSDataInteger(
iTotalNumberOfImages)
xsDataISPyBScreeningOutput.totalRotationRange = XSDataDouble(
fTotalRotationRange)
xsDataISPyBScreeningStrategyContainer.screeningStrategy = xsDataISPyBScreeningStrategy
# Assembly
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer(
)
xsDataISPyBScreeningOutputContainer.screeningOutput = xsDataISPyBScreeningOutput
if xsDataISPyBScreeningOutputLattice is not None:
xsDataISPyBScreeningOutputContainer.addScreeningOutputLattice(
xsDataISPyBScreeningOutputLattice)
if xsDataISPyBScreeningStrategyContainer is not None:
xsDataISPyBScreeningOutputContainer.addScreeningStrategyContainer(
xsDataISPyBScreeningStrategyContainer)
return xsDataISPyBScreeningOutputContainer
qMax = None
datapoint = numpy.loadtxt(self.strInFile)[firstPoint:lastPoint]
q = datapoint[:, 0]
I = datapoint[:, 1]
s = datapoint[:, 2]
if qMax is not None:
mask = (q < qMax)
q = q[mask]
I = I[mask]
s = s[mask]
xsd = XSDataInputSolutionScattering(experimentalDataQArray=EDUtilsArray.arrayToXSData(q / 10.), #from nm-1 not A-1
experimentalDataIArray=EDUtilsArray.arrayToXSData(I),
experimentalDataStdArray=EDUtilsArray.arrayToXSData(s),
title=XSDataString(title.strip()),
angularUnits=XSDataInteger(1))
if self.__class__.maxThreads is not None:
xsd.iNbThreads = XSDataInteger(self.__class__.maxThreads)
self.__edPluginExecSAS = self.loadPlugin(self.__strControlledPluginSAS)
self.__edPluginExecSAS.dataInput = xsd
self.__edPluginExecSAS.connectSUCCESS(self.doSuccessExecSAS)
self.__edPluginExecSAS.connectFAILURE(self.doFailureExecSAS)
self.__edPluginExecSAS.executeSynchronous()
if self.isFailure():
return
if self.dataInput.destinationDirectory is None:
outdir = os.path.join(os.path.dirname(os.path.dirname(self.strInFile)), "ednaSAS")
else:
outdir = self.dataInput.destinationDirectory.path.value
outdir = os.path.join(outdir, os.path.basename(os.path.splitext(self.strInFile)[0]))
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:
self.modify_strategy_option(diff_plan, "-DamPar")
# Characterisation type - SAD
if char_params.opt_sad:
if char_params.auto_res:
diff_plan.setAnomalousData(XSDataBoolean(True))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
self.modify_strategy_option(diff_plan, "-SAD yes")
diff_plan.setAimedResolution(XSDataDouble(char_params.sad_res))
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 create_autoproc_input(self, event, params):
"""Creates processing input xml
:param event: processing type (after, before, image)
:type event: str
:param params: collection parameters
:type params: dict
"""
xds_input_file_wait_timeout = 20
xds_input_file_wait_resolution = 1
file_name_timestamp = time.strftime("%Y%m%d_%H%M%S")
autoproc_path = params.get("xds_dir")
autoproc_xds_filename = os.path.join(autoproc_path, "XDS.INP")
autoproc_input_filename = os.path.join(\
autoproc_path,
"edna-autoproc-input-%s.xml" % \
file_name_timestamp)
autoproc_output_file_name = os.path.join(\
autoproc_path,
"edna-autoproc-results-%s.xml" % \
file_name_timestamp)
autoproc_input = XSDataAutoprocInput()
autoproc_xds_file = XSDataFile()
autoproc_xds_file.setPath(XSDataString(autoproc_xds_filename))
autoproc_input.setInput_file(autoproc_xds_file)
autoproc_output_file = XSDataFile()
autoproc_output_file.setPath(XSDataString(autoproc_output_file_name))
autoproc_input.setOutput_file(autoproc_output_file)
autoproc_input.setData_collection_id(\
XSDataInteger(params.get("collection_id")))
residues_num = float(params.get("residues", 0))
if residues_num != 0:
autoproc_input.setNres(XSDataDouble(residues_num))
space_group = params.get("sample_reference").get("spacegroup", "")
if len(space_group) > 0:
autoproc_input.setSpacegroup(XSDataString(space_group))
unit_cell = params.get("sample_reference").get("cell", "")
if len(unit_cell) > 0:
autoproc_input.setUnit_cell(XSDataString(unit_cell))
autoproc_input.setCc_half_cutoff(XSDataDouble(18.0))
#Maybe we have to check if directory is there.
#Maybe create dir with mxcube
xds_appeared = False
wait_xds_start = time.time()
logging.debug("EMBLAutoprocessing: Waiting for XDS.INP " +\
"file: %s" % autoproc_xds_filename)
while not xds_appeared and time.time() - wait_xds_start < xds_input_file_wait_timeout:
if os.path.exists(autoproc_xds_filename) and \
os.stat(autoproc_xds_filename).st_size > 0:
xds_appeared = True
logging.debug('EMBLAutoprocessing: XDS.INP file is there, size={0}'.\
format(os.stat(autoproc_xds_filename).st_size))
else:
os.system("ls %s> /dev/null"%(os.path.dirname(autoproc_path)))
gevent.sleep(xds_input_file_wait_resolution)
if not xds_appeared:
logging.error("EMBLAutoprocessing: XDS.INP file ({0}) failed " +\
"to appear after {1} seconds".\
format(autoproc_xds_filename, xds_input_file_wait_timeout))
return None, False
autoproc_input.exportToFile(autoproc_input_filename)
return autoproc_input_filename, True
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBGetSampleInformationv1_4.process")
# First get the image ID
xsDataInputGetSampleInformation = self.getDataInput()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForBLSampleWebServiceWsdl = Client(self.strToolsForBLSampleWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService)
iSampleId = self.getXSValue(xsDataInputGetSampleInformation.sampleId)
sampleInfo = clientToolsForBLSampleWebServiceWsdl.service.getSampleInformation(iSampleId)
self.DEBUG("Sample info from ISPyB: %r" % sampleInfo)
if sampleInfo is not None:
if "code" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.code = XSDataString(sampleInfo.code)
if "cellA" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellA = XSDataDouble(sampleInfo.cellA)
if "cellB" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellB = XSDataDouble(sampleInfo.cellB)
if "cellC" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellC = XSDataDouble(sampleInfo.cellC)
if "cellAlpha" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellAlpha = XSDataDouble(sampleInfo.cellAlpha)
if "cellBeta" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellBeta = XSDataDouble(sampleInfo.cellBeta)
if "cellGamma" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellGamma = XSDataDouble(sampleInfo.cellGamma)
if "containerSampleChangerLocation" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.containerSampleChangerLocation = XSDataString(sampleInfo.containerSampleChangerLocation)
if "crystalSpaceGroup" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.crystalSpaceGroup = XSDataString(sampleInfo.crystalSpaceGroup)
if "experimentType" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.experimentType = XSDataString(sampleInfo.experimentType)
if "holderLength" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.holderLength = XSDataDouble(sampleInfo.holderLength)
if "minimalResolution" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.minimalResolution = XSDataDouble(sampleInfo.minimalResolution)
if "proteinAcronym" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.proteinAcronym = XSDataString(sampleInfo.proteinAcronym)
if "sampleId" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleId = XSDataInteger(sampleInfo.sampleId)
if "sampleLocation" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleLocation = XSDataString(sampleInfo.sampleLocation)
if "sampleName" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleName = XSDataString(sampleInfo.sampleName)
if "diffractionPlan" in sampleInfo:
xsDataISPyBDiffractionPlan = XSDataISPyBDiffractionPlan()
if "aimedCompleteness" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedCompleteness = XSDataDouble(sampleInfo.diffractionPlan.aimedCompleteness)
if "aimedIOverSigmaAtHighestResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedIOverSigmaAtHighestResolution = XSDataDouble(sampleInfo.diffractionPlan.aimedIOverSigmaAtHighestResolution)
if "aimedMultiplicity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedMultiplicity = XSDataDouble(sampleInfo.diffractionPlan.aimedMultiplicity)
if "aimedResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedResolution = XSDataDouble(sampleInfo.diffractionPlan.aimedResolution)
if "anomalousData" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.anomalousData = XSDataBoolean(sampleInfo.diffractionPlan.anomalousData)
if "comments" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.comments = XSDataString(sampleInfo.diffractionPlan.comments)
if "complexity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.complexity = XSDataString(sampleInfo.diffractionPlan.complexity)
if "diffractionPlanId" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.diffractionPlanId = XSDataInteger(sampleInfo.diffractionPlan.diffractionPlanId)
if "estimateRadiationDamage" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.estimateRadiationDamage = XSDataBoolean(sampleInfo.diffractionPlan.estimateRadiationDamage)
if "experimentKind" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.experimentKind = XSDataString(sampleInfo.diffractionPlan.experimentKind)
if "exposureTime" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.exposureTime = XSDataDouble(sampleInfo.diffractionPlan.exposureTime)
if "forcedSpaceGroup" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.forcedSpaceGroup = XSDataString(sampleInfo.diffractionPlan.forcedSpaceGroup)
if "kappaStrategyOption" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.kappaStrategyOption = XSDataString(sampleInfo.diffractionPlan.kappaStrategyOption)
if "maxDimAccrossSpindleAxis" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.maxDimAccrossSpindleAxis = XSDataDouble(sampleInfo.diffractionPlan.maxDimAccrossSpindleAxis)
if "maximalResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.maximalResolution = XSDataDouble(sampleInfo.diffractionPlan.maximalResolution)
if "minDimAccrossSpindleAxis" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.minDimAccrossSpindleAxis = XSDataDouble(sampleInfo.diffractionPlan.minDimAccrossSpindleAxis)
if "minimalResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.minimalResolution = XSDataDouble(sampleInfo.diffractionPlan.minimalResolution)
if "numberOfPositions" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.numberOfPositions = XSDataInteger(sampleInfo.diffractionPlan.numberOfPositions)
if "observedResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.observedResolution = XSDataDouble(sampleInfo.diffractionPlan.observedResolution)
if "oscillationRange" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.oscillationRange = XSDataDouble(sampleInfo.diffractionPlan.oscillationRange)
if "preferredBeamSizeX" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.preferredBeamSizeX = XSDataDouble(sampleInfo.diffractionPlan.preferredBeamSizeX)
if "preferredBeamSizeY" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.preferredBeamSizeY = XSDataDouble(sampleInfo.diffractionPlan.preferredBeamSizeY)
if "radiationSensitivity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivity = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivity)
if "radiationSensitivityBeta" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivityBeta = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivityBeta)
if "radiationSensitivityGamma" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivityGamma = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivityGamma)
if "requiredCompleteness" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredCompleteness = XSDataDouble(sampleInfo.diffractionPlan.requiredCompleteness)
if "requiredMultiplicity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredMultiplicity = XSDataDouble(sampleInfo.diffractionPlan.requiredMultiplicity)
if "requiredResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredResolution = XSDataDouble(sampleInfo.diffractionPlan.requiredResolution)
if "screeningResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.screeningResolution = XSDataDouble(sampleInfo.diffractionPlan.screeningResolution)
if "anomalousScatterer" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.anomalousScatterer = XSDataString(sampleInfo.diffractionPlan.anomalousScatterer)
if "strategyOption" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.strategyOption = XSDataString(sampleInfo.diffractionPlan.strategyOption)
self.xsDataResultISPyBGetSampleInformation.diffractionPlan = xsDataISPyBDiffractionPlan
self.DEBUG("EDPluginISPyBGetSampleInformationv1_4.process: result=%s" % pprint.pformat(self.xsDataResultISPyBGetSampleInformation))
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'number':
obj_ = XSDataInteger()
obj_.build(child_)
self.setNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'scale':
obj_ = XSDataDouble()
obj_.build(child_)
self.setScale(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'bfactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setBfactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'resolution':
obj_ = XSDataDouble()
obj_.build(child_)
self.setResolution(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'correlation':
obj_ = XSDataDouble()
obj_.build(child_)
self.setCorrelation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'rfactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setRfactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'b_coef':
obj_ = XSDataDouble()
obj_.build(child_)
self.setB_coef(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'b_cryst':
obj_ = XSDataDouble()
obj_.build(child_)
self.setB_cryst(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'esitmate':
obj_ = XSDataDouble()
obj_.build(child_)
self.setEsitmate(obj_)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG(
"EDPluginControlPyarchThumbnailGeneratorv1_0.preProcess")
# Check that the input image exists and is of the expected type
strPathToDiffractionImage = self.getDataInput().getDiffractionImage(
).getPath().getValue()
strImageFileNameExtension = os.path.splitext(
strPathToDiffractionImage)[1]
if not strImageFileNameExtension in [
".img", ".marccd", ".mccd", ".cbf"
]:
EDVerbose.error(
"Unknown image file name extension for pyarch thumbnail generator: %s"
% strPathToDiffractionImage)
self.setFailure()
else:
# Load the waitFile plugin
xsDataInputWaitFile = XSDataInputWaitFile()
xsDataInputWaitFile.setExpectedSize(
XSDataInteger(self.iExpectedSize))
xsDataInputWaitFile.setExpectedFile(
self.getDataInput().getDiffractionImage())
if self.getDataInput().getWaitForFileTimeOut():
xsDataInputWaitFile.setTimeOut(
self.getDataInput().getWaitForFileTimeOut())
self.edPluginWaitFile = EDPluginWaitFile()
self.edPluginWaitFile.setDataInput(xsDataInputWaitFile)
# Load the execution plugin
self.edPluginExecThumbnail = self.loadPlugin(
self.strExecThumbnailPluginName)
xsDataInputExecThumbnail = XSDataInputExecThumbnail()
xsDataInputExecThumbnail.setInputImagePath(
self.getDataInput().getDiffractionImage())
xsDataInputExecThumbnail.setLevelsInvert(XSDataBoolean(True))
xsDataInputExecThumbnail.setLevelsMin(XSDataDoubleWithUnit(0.0))
xsDataDoubleWithUnitLevelsMax = XSDataDoubleWithUnit(99.95)
xsDataDoubleWithUnitLevelsMax.setUnit(XSDataString("%"))
xsDataInputExecThumbnail.setLevelsMax(
xsDataDoubleWithUnitLevelsMax)
xsDataInputExecThumbnail.setFilterDilatation([XSDataInteger(4)])
xsDataInputExecThumbnail.setLevelsColorize(XSDataBoolean(False))
xsDataInputExecThumbnail.setThumbHeight(XSDataInteger(1024))
xsDataInputExecThumbnail.setThumbWidth(XSDataInteger(1024))
xsDataInputExecThumbnail.setKeepRatio(XSDataBoolean(False))
# Output path
strImageNameWithoutExt = os.path.basename(
os.path.splitext(strPathToDiffractionImage)[0])
strImageDirname = os.path.dirname(strPathToDiffractionImage)
if self.getDataInput().getForcedOutputDirectory():
strForcedOutputDirectory = self.getDataInput(
).getForcedOutputDirectory().getPath().getValue()
if not os.access(strForcedOutputDirectory, os.W_OK):
EDVerbose.error(
"Cannot write to forced output directory : %s" %
strForcedOutputDirectory)
self.setFailure()
else:
self.strOutputPathWithoutExtension = os.path.join(
strForcedOutputDirectory, strImageNameWithoutExt)
else:
# Try to store in the ESRF pyarch directory
strOutputDirname = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
strImageDirname)
# Check that output pyarch path exists and is writeable:
bIsOk = False
if strOutputDirname:
if not os.path.exists(strOutputDirname):
# Try to create the directory
try:
os.makedirs(strOutputDirname)
bIsOk = True
except BaseException, e:
EDVerbose.WARNING(
"Couldn't create the directory %s" %
strOutputDirname)
elif os.access(strOutputDirname, os.W_OK):
bIsOk = True
if not bIsOk:
EDVerbose.warning("Cannot write to pyarch directory: %s" %
strOutputDirname)
strOutputDirname = tempfile.mkdtemp(
"", "EDPluginPyarchThumbnailv10_", "/tmp")
EDVerbose.warning("Writing thumbnail images to: %s" %
strOutputDirname)
self.strOutputPathWithoutExtension = os.path.join(
strOutputDirname, strImageNameWithoutExt)
self.strOutputPath = os.path.join(
self.strOutputPathWithoutExtension + ".jpeg")
xsDataInputExecThumbnail.setOutputPath(
XSDataFile(XSDataString(self.strOutputPath)))
self.edPluginExecThumbnail.setDataInput(xsDataInputExecThumbnail)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'number':
obj_ = XSDataInteger()
obj_.build(child_)
self.setNumber(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'spots_num_of':
obj_ = XSDataInteger()
obj_.build(child_)
self.setSpots_num_of(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'spots_int_aver':
obj_ = XSDataDouble()
obj_.build(child_)
self.setSpots_int_aver(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'spots_resolution':
obj_ = XSDataDouble()
obj_.build(child_)
self.setSpots_resolution(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'powder_wilson_scale':
obj_ = XSDataDouble()
obj_.build(child_)
self.setPowder_wilson_scale(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'powder_wilson_bfactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setPowder_wilson_bfactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'powder_wilson_resolution':
obj_ = XSDataDouble()
obj_.build(child_)
self.setPowder_wilson_resolution(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'powder_wilson_correlation':
obj_ = XSDataDouble()
obj_.build(child_)
self.setPowder_wilson_correlation(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'powder_wilson_rfactor':
obj_ = XSDataDouble()
obj_.build(child_)
self.setPowder_wilson_rfactor(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'score':
obj_ = XSDataDouble()
obj_.build(child_)
self.setScore(obj_)
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataCollectionId':
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'processDirectory':
obj_ = XSDataFile()
obj_.build(child_)
self.setProcessDirectory(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'geomFile':
obj_ = XSDataString()
obj_.build(child_)
self.setGeomFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'cellFile':
obj_ = XSDataString()
obj_.build(child_)
self.setCellFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imagesFullPath':
obj_ = XSDataString()
obj_.build(child_)
self.setImagesFullPath(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'streamFile':
obj_ = XSDataString()
obj_.build(child_)
self.setStreamFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'hklFile':
obj_ = XSDataString()
obj_.build(child_)
self.setHklFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'mtzFile':
obj_ = XSDataString()
obj_.build(child_)
self.setMtzFile(obj_)
XSDataInput.buildChildren(self, child_, nodeName_)
