def getH5FilePath(self, filePath, batchSize=1):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath), h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_000001.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath), h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_0.process")
xsDataResultControlDozor = XSDataResultControlDozor()
for xsDataFile in self.dataInput.image:
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataDouble(5.0)
xsDataInputDozor.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputDozor.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
xsDataInputDozor.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputDozor.imageStep : XSDataDouble optional
xsDataInputDozor.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputDozor.firstImageNumber = subWedge.image[0].number
xsDataInputDozor.numberImages = XSDataInteger(1)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputDozor.nameTemplateImage = XSDataString(os.path.join(os.path.dirname(strFileName), strXDSTemplate))
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor")
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.executeSynchronous()
if edPluginDozor.dataOutput.imageDozor != []:
xsDataResultDozor = edPluginDozor.dataOutput.imageDozor[0]
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.image = xsDataFile
xsDataControlImageDozor.spots_num_of = xsDataResultDozor.spots_num_of
xsDataControlImageDozor.spots_int_aver = xsDataResultDozor.spots_int_aver
xsDataControlImageDozor.spots_resolution = xsDataResultDozor.spots_resolution
xsDataControlImageDozor.powder_wilson_scale = xsDataResultDozor.powder_wilson_scale
xsDataControlImageDozor.powder_wilson_bfactor = xsDataResultDozor.powder_wilson_bfactor
xsDataControlImageDozor.powder_wilson_resolution = xsDataResultDozor.powder_wilson_resolution
xsDataControlImageDozor.powder_wilson_correlation = xsDataResultDozor.powder_wilson_correlation
xsDataControlImageDozor.powder_wilson_rfactor = xsDataResultDozor.powder_wilson_rfactor
xsDataControlImageDozor.score = xsDataResultDozor.score
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
self.dataOutput = xsDataResultControlDozor
def getH5FilePath(self, filePath, batchSize=1):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(
prefix=prefix, h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath),
h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_000001.h5".format(
prefix=prefix, h5FileNumber=h5FileNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath),
h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlBackground3Dv1_0.process")
xsDataResultControlBackground3D = XSDataResultControlBackground3D()
for xsDataFile in self.dataInput.image:
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputBackground3D = XSDataInputBackground3D()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputBackground3D.detectorType = detector.type
xsDataInputBackground3D.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputBackground3D.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputBackground3D.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputBackground3D.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputBackground3D.orgx = XSDataDouble(orgx)
xsDataInputBackground3D.orgy = XSDataDouble(orgy)
xsDataInputBackground3D.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputBackground3D.imageStep : XSDataDouble optional
xsDataInputBackground3D.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputBackground3D.firstImageNumber = subWedge.image[0].number
xsDataInputBackground3D.numberImages = XSDataInteger(1)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputBackground3D.nameTemplateImage = XSDataString(os.path.join(os.path.dirname(strFileName), strXDSTemplate))
edPluginBackground3D = self.loadPlugin(self.strEDPluginBackground3DName, "Background3D")
edPluginBackground3D.dataInput = xsDataInputBackground3D
edPluginBackground3D.executeSynchronous()
if edPluginBackground3D.dataOutput.imageBackground != []:
xsDataResultBackground3D = edPluginBackground3D.dataOutput.imageBackground[0]
xsDataControlImageBackground3D = XSDataControlImageBackground3D()
xsDataControlImageBackground3D.image = xsDataFile
xsDataControlImageBackground3D.scale = xsDataResultBackground3D.scale
xsDataControlImageBackground3D.bfactor = xsDataResultBackground3D.bfactor
xsDataControlImageBackground3D.resolution = xsDataResultBackground3D.resolution
xsDataControlImageBackground3D.correlation = xsDataResultBackground3D.correlation
xsDataControlImageBackground3D.rfactor = xsDataResultBackground3D.rfactor
xsDataControlImageBackground3D.b_coef = xsDataResultBackground3D.b_coef
xsDataControlImageBackground3D.b_cryst = xsDataResultBackground3D.b_cryst
xsDataControlImageBackground3D.estimate = xsDataResultBackground3D.estimate
xsDataResultControlBackground3D.addImageBackground(xsDataControlImageBackground3D)
self.dataOutput = xsDataResultControlBackground3D
def testGetImageNumber(self):
"""
Testing retrieving the image number from a image filename
"""
iImageNumber = EDUtilsImage.getImageNumber(self.__strFileName)
iReference = 1
EDAssert.equal(iReference, iImageNumber)
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection()
if xsDataCollection is not None:
firstSubWedge = xsDataCollection.subWedge[0]
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataBeam = firstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self.fMinTransmission:
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.page.font(_color="red", size="+2")
self.page.i()
self.page.h2(strWarningMessage1+"<br>"+strWarningMessage2)
self.page.i.close()
self.page.font.close()
self.page.h2( "Data collection info" )
firstImage = firstSubWedge.image[0]
strDate = firstImage.date.value
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
self.page.table( class_='dataCollectionInfo', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER")
self.page.th("Data collection date", bgcolor_=self.strTableColourTitle2)
self.page.th(strDate, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Image prefix", bgcolor_=self.strTableColourTitle2)
self.page.th(strPrefix, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Directory", bgcolor_=self.strTableColourTitle2)
self.page.th(strDirName, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.table.close()
def createImageDict(self, _xsDataControlDozorInput):
# Create dictionary of all images with the image number as key
dictImage = {}
if len(_xsDataControlDozorInput.image) > 0:
listImage = _xsDataControlDozorInput.image
pathToFirstImage = listImage[0].path.value
self.directory = os.path.dirname(pathToFirstImage)
self.template = os.path.basename(pathToFirstImage).replace(
"0001", "####")
else:
# Create list of images
listImage = []
self.directory = _xsDataControlDozorInput.directory.path.value
self.template = _xsDataControlDozorInput.template.value
startNo = _xsDataControlDozorInput.startNo.value
endNo = _xsDataControlDozorInput.endNo.value
for imageIndex in range(startNo, endNo + 1):
imageName = self.template % imageIndex
imagePath = os.path.join(self.directory, imageName)
listImage.append(XSDataFile(XSDataString(imagePath)))
for image in listImage:
imagePath = image.path.value
imageNo = EDUtilsImage.getImageNumber(imagePath)
dictImage[imageNo] = image
return dictImage
def createPyarchHtmlDirectoryPath(_xsDataCollection):
"""
This method creates a directory path for pyarch: in the same directory were the
images are located a new directory is created with the following convention:
edna_html_prefix_runNumber
"""
# First extract all reference image directory paths and names
listImageDirectoryPath = []
listImagePrefix = []
for xsDataSubWedge in _xsDataCollection.getSubWedge():
for xsDataImage in xsDataSubWedge.getImage():
strImagePath = xsDataImage.getPath().getValue()
listImageDirectoryPath.append(os.path.dirname(strImagePath))
listImagePrefix.append(EDUtilsImage.getPrefix(strImagePath))
# TODO: Check that all paths and prefixes are the same
strImageDirectory = listImageDirectoryPath[0]
strPrefix = listImagePrefix[0]
# Remove any "ref-" or "postref-" from the prefix in order to make it fully
# compatitble with DNA standards:
if (strPrefix is not None):
if (strPrefix.startswith("ref-")):
strPrefix = strPrefix[4:]
elif (strPrefix.startswith("postref-")):
strPrefix = strPrefix[8:]
strHtmlDirectoryPath = os.path.join(strImageDirectory,
"%s_dnafiles" % strPrefix)
strPyarchHtmlDirectoryPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
strHtmlDirectoryPath)
return strPyarchHtmlDirectoryPath
def testGetImageNumber(self):
"""
Testing retrieving the image number from a image filename
"""
iImageNumber = EDUtilsImage.getImageNumber(self.__strFileName)
iReference = 1
EDAssert.equal(iReference, iImageNumber)
def createDNAFileDirectoryPath(self, _xsDataResultCharacterisation):
"""
This method creates a "DNA" style directory path, i.e. in the same directory were the
images are located a new directory is created with the following convention:
dnafiles_prefix_runNumber
The path to this directory is returned if the directory was successfully created.
"""
# First extract all reference image directory paths and names
xsDataCollection = _xsDataResultCharacterisation.getDataCollection()
listImageDirectoryPath = []
listImagePrefix = []
for xsDataSubWedge in xsDataCollection.getSubWedge():
for xsDataImage in xsDataSubWedge.getImage():
strImagePath = xsDataImage.getPath().getValue()
listImageDirectoryPath.append(os.path.dirname(strImagePath))
listImagePrefix.append(EDUtilsImage.getPrefix(strImagePath))
# TODO: Check that all paths and prefixes are the same
strImageDirectory = listImageDirectoryPath[0]
strPrefix = listImagePrefix[0]
# Remove any "ref-" or "postref-" from the prefix in order to make it fully
# compatitble with DNA standards:
if (strPrefix is not None):
if (strPrefix.startswith("ref-")):
strPrefix = strPrefix[4:]
elif (strPrefix.startswith("postref-")):
strPrefix = strPrefix[8:]
strDNAFileDirectoryPath = os.path.join(strImageDirectory,
"%s_dnafiles" % strPrefix)
return strDNAFileDirectoryPath
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection()
if xsDataCollection is not None:
firstSubWedge = xsDataCollection.subWedge[0]
firstImage = firstSubWedge.image[0]
if firstImage.date is not None:
strDate = firstImage.date.value
else:
strDate = "-----"
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
dictTable = {"type": "table",
"title": "Data collection info",
"columns": [],
"data": []}
listRow = []
dictTable["columns"].append("Data collection date")
listRow.append(strDate)
dictTable["columns"].append("Image prefix")
listRow.append(strPrefix)
dictTable["columns"].append("Directory")
listRow.append(strDirName)
dictTable["data"].append(listRow)
#
self.workflowStepReport.addTable("Data collection info",
dictTable["columns"],
dictTable["data"],
orientation="vertical")
def createPyarchHtmlDirectoryPath(_xsDataCollection):
"""
This method creates a directory path for pyarch: in the same directory were the
images are located a new directory is created with the following convention:
edna_html_prefix_runNumber
"""
# First extract all reference image directory paths and names
listImageDirectoryPath = []
listImagePrefix = []
for xsDataSubWedge in _xsDataCollection.getSubWedge():
for xsDataImage in xsDataSubWedge.getImage():
strImagePath = xsDataImage.getPath().getValue()
listImageDirectoryPath.append(os.path.dirname(strImagePath))
listImagePrefix.append(EDUtilsImage.getPrefix(strImagePath))
# TODO: Check that all paths and prefixes are the same
strImageDirectory = listImageDirectoryPath[0]
strPrefix = listImagePrefix[0]
# Remove any "ref-" or "postref-" from the prefix in order to make it fully
# compatitble with DNA standards:
if (strPrefix is not None):
if (strPrefix.startswith("ref-")):
strPrefix = strPrefix[4:]
elif (strPrefix.startswith("postref-")):
strPrefix = strPrefix[8:]
strHtmlDirectoryPath = os.path.join(strImageDirectory, "%s_dnafiles" % strPrefix)
strPyarchHtmlDirectoryPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strHtmlDirectoryPath)
return strPyarchHtmlDirectoryPath
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecXDSAPPv1_0.postProcess")
# Populate the results
prefixRunNumber = EDUtilsImage.getPrefix(self.dataInput.image.path.value)
xsDataResultXDSAPP = self.parseOutputDirectory(self.getWorkingDirectory(), prefixRunNumber)
self.dataOutput = xsDataResultXDSAPP
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection()
if xsDataCollection is not None:
self.page.h2( "Data collection info" )
firstSubWedge = xsDataCollection.subWedge[0]
firstImage = firstSubWedge.image[0]
strDate = None
if not firstImage.date is None:
strDate = firstImage.date.value
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
self.page.table( class_='dataCollectionInfo', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER")
self.page.th("Data collection date", bgcolor_=self.strTableColourTitle2)
if not strDate is None:
self.page.th(strDate, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Image prefix", bgcolor_=self.strTableColourTitle2)
self.page.th(strPrefix, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Directory", bgcolor_=self.strTableColourTitle2)
self.page.th(strDirName, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.table.close()
def createDNAFileDirectoryPath(self, _xsDataResultCharacterisation):
"""
This method creates a "DNA" style directory path, i.e. in the same directory were the
images are located a new directory is created with the following convention:
dnafiles_prefix_runNumber
The path to this directory is returned if the directory was successfully created.
"""
# First extract all reference image directory paths and names
xsDataCollection = _xsDataResultCharacterisation.getDataCollection()
listImageDirectoryPath = []
listImagePrefix = []
for xsDataSubWedge in xsDataCollection.getSubWedge():
for xsDataImage in xsDataSubWedge.getImage():
strImagePath = xsDataImage.getPath().getValue()
listImageDirectoryPath.append(os.path.dirname(strImagePath))
listImagePrefix.append(EDUtilsImage.getPrefix(strImagePath))
# TODO: Check that all paths and prefixes are the same
strImageDirectory = listImageDirectoryPath[0]
strPrefix = listImagePrefix[0]
# Remove any "ref-" or "postref-" from the prefix in order to make it fully
# compatitble with DNA standards:
if (strPrefix is not None):
if (strPrefix.startswith("ref-")):
strPrefix = strPrefix[4:]
elif (strPrefix.startswith("postref-")):
strPrefix = strPrefix[8:]
strDNAFileDirectoryPath = os.path.join(strImageDirectory, "%s_dnafiles" % strPrefix)
return strDNAFileDirectoryPath
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection(
)
if xsDataCollection is not None:
firstSubWedge = xsDataCollection.subWedge[0]
firstImage = firstSubWedge.image[0]
if firstImage.date is not None:
strDate = firstImage.date.value
else:
strDate = "-----"
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
dictTable = {
"type": "table",
"title": "Data collection info",
"columns": [],
"data": []
}
listRow = []
dictTable["columns"].append("Data collection date")
listRow.append(strDate)
dictTable["columns"].append("Image prefix")
listRow.append(strPrefix)
dictTable["columns"].append("Directory")
listRow.append(strDirName)
dictTable["data"].append(listRow)
#
self.workflowStepReport.addTable("Data collection info",
dictTable["columns"],
dictTable["data"],
orientation="vertical")
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection(
)
if xsDataCollection is not None:
self.page.h2("Data collection info")
firstSubWedge = xsDataCollection.subWedge[0]
firstImage = firstSubWedge.image[0]
strDate = None
if not firstImage.date is None:
strDate = firstImage.date.value
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
self.page.table(class_='dataCollectionInfo',
border_="1",
cellpadding_="0")
self.page.tr(align_="CENTER")
self.page.th("Data collection date",
bgcolor_=self.strTableColourTitle2)
if not strDate is None:
self.page.th(strDate, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Image prefix", bgcolor_=self.strTableColourTitle2)
self.page.th(strPrefix, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Directory", bgcolor_=self.strTableColourTitle2)
self.page.th(strDirName, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.table.close()
def doSuccessMXWaitFile(self, _edPlugin=None):
self.DEBUG("EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile")
# Check that the image is really there
if not self.edPluginMXWaitFile.dataOutput.timedOut.value:
# Workaround for ESRF lag problem
if EDUtilsPath.isESRF():
time.sleep(2)
if self.isH5:
diffractionImagePath = self.dataInput.diffractionImage.path.value
imageNumber = EDUtilsImage.getImageNumber(diffractionImagePath)
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(diffractionImagePath))
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(self.h5FileNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = None
xsDataInputControlH5ToCBF.forcedOutputDirectory = XSDataFile(XSDataString(self.getWorkingDirectory()))
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_{0:04d}".format(imageNumber))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
self.edPluginExecThumbnail.dataInput.image = cbfFile
# The image is here - make the first thumbnail
self.edPluginExecThumbnail.connectSUCCESS(self.doSuccessExecThumbnail)
self.edPluginExecThumbnail.connectFAILURE(self.doFailureExecThumbnail)
self.edPluginExecThumbnail.executeSynchronous()
else:
self.error("Time-out while waiting for image!")
self.setFailure()
def doSuccessActionOldSubWedgeAssemble(self, _edPlugin=None):
"""
- gets the result from the old assembler
- converts it to DMv2
- reads DC descriptor file prepared by the BCM
- merges the info together
"""
EDVerbose.DEBUG(
"EDPluginControlSubWedgeAssemblyv2_0.doSuccessActionSubWedgeMerge")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlSubWedgeAssemblyv2_0.doSuccessActionOldSubWedgeAssemble"
)
if not _edPlugin.isFailure():
# getting the result from the old assembler
self.xsDataResultSubWedgeAssemble = _edPlugin.getDataOutput()
# converts it to DMv2
# reads DC descriptor file(s) prepared by the BCM
swList = self.xsDataResultSubWedgeAssemble.getSubWedge()
try:
for sw in swList:
# get filename
imgFname = sw.getImage()[0].getPath().getValue()
strMOSFLMTemplate = os.path.dirname(
imgFname) + '/edna_' + EDUtilsImage.getTemplate(
imgFname, "#")
# print strMOSFLMTemplate
# read file in
#self.xsDatacollection_v2 = XSDataCollection_v2()
self.xsDatacollection_v2 = XSDataMXv2.XSDataCollection.parseFile(
strMOSFLMTemplate)
except IOError:
# TEMP: generates the file to be read in
##PARAMS
calibDate = '2009-12-10'
omegaR = (0, 0, 1)
kappaR = (0, 0.707106781187, 0.707106781187)
phiR = (0, 0, 1)
beamD = (1, 0, 0)
polarisationP = (0, 1, 0)
exposuretime = 1.0
imagewidth = 1.0
numberimages = 1
wavelength = 1.0
OmegaV = 0.0
KappaV = 90.0
PhiV = 40.0
imgFnames = []
imgFnames.append(
self.xsDataResultSubWedgeAssemble.getSubWedge()
[0].getImage()[0].getPath().getValue())
self.generateDataCollectionDescriptorForSubWedge(
calibDate, omegaR, kappaR, phiR, beamD, polarisationP,
exposuretime, imagewidth, numberimages, wavelength, OmegaV,
KappaV, PhiV, imgFnames)
def testGetTemplateQuestionMark(self):
"""
Testing retrieving the image number from a image filename
"""
strSymbol = "?"
strTemplate = EDUtilsImage.getTemplate(self.__strFileName, strSymbol)
strTemplateReference = "ref-testscale_1_???.img"
EDAssert.equal(strTemplateReference, strTemplate)
def testGetTemplateQuestionMark(self):
"""
Testing retrieving the image number from a image filename
"""
strSymbol = "?"
strTemplate = EDUtilsImage.getTemplate(self.__strFileName, strSymbol)
strTemplateReference = "ref-testscale_1_???.img"
EDAssert.equal(strTemplateReference, strTemplate)
def getH5FilePath(self, filePath, batchSize=1, isFastMesh=False):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
if isFastMesh:
h5ImageNumber = int((imageNumber - 1) / 100) + 1
h5FileNumber = 1
else:
h5ImageNumber = 1
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath), h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_{h5ImageNumber:06d}.h5".format(prefix=prefix,
h5FileNumber=h5FileNumber,
h5ImageNumber=h5ImageNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath), h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecXDSAPPv1_0.postProcess")
# Populate the results
prefixRunNumber = EDUtilsImage.getPrefix(
self.dataInput.image.path.value)
xsDataResultXDSAPP = self.parseOutputDirectory(
self.getWorkingDirectory(), prefixRunNumber)
self.dataOutput = xsDataResultXDSAPP
def getH5FilePath(self, filePath, batchSize=1, isFastMesh=False):
imageNumber = EDUtilsImage.getImageNumber(filePath)
prefix = EDUtilsImage.getPrefix(filePath)
if isFastMesh:
h5ImageNumber = int((imageNumber - 1) / 100) + 1
h5FileNumber = 1
else:
h5ImageNumber = 1
h5FileNumber = int((imageNumber - 1) / batchSize) * batchSize + 1
h5MasterFileName = "{prefix}_{h5FileNumber}_master.h5".format(
prefix=prefix, h5FileNumber=h5FileNumber)
h5MasterFilePath = os.path.join(os.path.dirname(filePath),
h5MasterFileName)
h5DataFileName = "{prefix}_{h5FileNumber}_data_{h5ImageNumber:06d}.h5".format(
prefix=prefix,
h5FileNumber=h5FileNumber,
h5ImageNumber=h5ImageNumber)
h5DataFilePath = os.path.join(os.path.dirname(filePath),
h5DataFileName)
return h5MasterFilePath, h5DataFilePath, h5FileNumber
def getBeamlineProposalFromPath(self, _strPathToImage):
"""ESRF specific code for extracting the beamline name and prefix from the path"""
listPath = _strPathToImage.split("/")
strPrefix = EDUtilsImage.getPrefix(_strPathToImage).replace("ref-", "")
if listPath[2] == "visitor":
strBeamline = listPath[4]
strProposal = listPath[3]
elif listPath[3] == "inhouse":
strBeamline = listPath[2]
strProposal = listPath[4]
else:
strBeamline = "nobeamline"
strProposal = "noproposal"
return (strBeamline, strProposal, strPrefix)
def getBeamlineProposalFromPath(self, _strPathToImage):
"""ESRF specific code for extracting the beamline name and prefix from the path"""
listPath = _strPathToImage.split("/")
strPrefix = EDUtilsImage.getPrefix(_strPathToImage).replace("ref-", "")
if listPath[2] == "visitor":
strBeamline = listPath[4]
strProposal = listPath[3]
elif listPath[3] == "inhouse":
strBeamline = listPath[2]
strProposal = listPath[4]
else:
strBeamline = "nobeamline"
strProposal = "noproposal"
return (strBeamline, strProposal, strPrefix)
def doSuccessActionOldSubWedgeAssemble(self, _edPlugin=None):
"""
- gets the result from the old assembler
- converts it to DMv2
- reads DC descriptor file prepared by the BCM
- merges the info together
"""
EDVerbose.DEBUG("EDPluginControlSubWedgeAssemblyv2_0.doSuccessActionSubWedgeMerge")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlSubWedgeAssemblyv2_0.doSuccessActionOldSubWedgeAssemble")
if not _edPlugin.isFailure():
# getting the result from the old assembler
self.xsDataResultSubWedgeAssemble = _edPlugin.getDataOutput()
# converts it to DMv2
# reads DC descriptor file(s) prepared by the BCM
swList = self.xsDataResultSubWedgeAssemble.getSubWedge()
try:
for sw in swList:
# get filename
imgFname = sw.getImage()[0].getPath().getValue()
strMOSFLMTemplate = os.path.dirname(imgFname) + '/edna_' + EDUtilsImage.getTemplate(imgFname, "#")
# print strMOSFLMTemplate
# read file in
#self.xsDatacollection_v2 = XSDataCollection_v2()
self.xsDatacollection_v2 = XSDataMXv2.XSDataCollection.parseFile(strMOSFLMTemplate)
except IOError:
# TEMP: generates the file to be read in
##PARAMS
calibDate = '2009-12-10'
omegaR = (0, 0, 1)
kappaR = (0, 0.707106781187, 0.707106781187)
phiR = (0, 0, 1)
beamD = (1, 0, 0)
polarisationP = (0, 1, 0)
exposuretime = 1.0
imagewidth = 1.0
numberimages = 1
wavelength = 1.0
OmegaV = 0.0
KappaV = 90.0
PhiV = 40.0
imgFnames = []
imgFnames.append(self.xsDataResultSubWedgeAssemble.getSubWedge()[0].getImage()[0].getPath().getValue())
self.generateDataCollectionDescriptorForSubWedge(calibDate, omegaR, kappaR, phiR, beamD, polarisationP, exposuretime, imagewidth, numberimages, wavelength, OmegaV, KappaV, PhiV, imgFnames)
def createImageDictFromISPyB(self, _ispybDataCollection):
# Create dictionary of all images with the image number as key
dictImage = {}
# Create list of images
listImage = []
self.directory = _ispybDataCollection.imageDirectory
self.template = _ispybDataCollection.fileTemplate
startNo = _ispybDataCollection.startImageNumber
endNo = _ispybDataCollection.startImageNumber + _ispybDataCollection.numberOfImages - 1
for imageIndex in range(startNo, endNo + 1):
imageName = self.template % imageIndex
imagePath = os.path.join(self.directory, imageName)
listImage.append(XSDataFile(XSDataString(imagePath)))
for image in listImage:
imagePath = image.path.value
imageNo = EDUtilsImage.getImageNumber(imagePath)
dictImage[imageNo] = image
return dictImage
def doSuccessMXWaitFile(self, _edPlugin=None):
self.DEBUG(
"EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlID29CreateThumbnailv1_0.doSuccessMXWaitFile")
# Check that the image is really there
if not self.edPluginMXWaitFile.dataOutput.timedOut.value:
# Workaround for ESRF lag problem
if EDUtilsPath.isESRF():
time.sleep(2)
if self.isH5:
diffractionImagePath = self.dataInput.diffractionImage.path.value
imageNumber = EDUtilsImage.getImageNumber(
diffractionImagePath)
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(
XSDataString(diffractionImagePath))
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(
imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(
self.h5FileNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = None
xsDataInputControlH5ToCBF.forcedOutputDirectory = XSDataFile(
XSDataString(self.getWorkingDirectory()))
edPluginControlH5ToCBF = self.loadPlugin(
self.strPluginControlH5ToCBF,
"ControlH5ToCBF_{0:04d}".format(imageNumber))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
self.edPluginExecThumbnail.dataInput.image = cbfFile
# The image is here - make the first thumbnail
self.edPluginExecThumbnail.connectSUCCESS(
self.doSuccessExecThumbnail)
self.edPluginExecThumbnail.connectFAILURE(
self.doFailureExecThumbnail)
self.edPluginExecThumbnail.executeSynchronous()
else:
self.error("Time-out while waiting for image!")
self.setFailure()
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
self.xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
if xsDataFile.path.value.endswith(".h5"):
self.bIsEigerDetector = True
self.xsDataFirstImage = xsDataFile
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(xsDataFile.path)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(
EDUtilsImage.getImageNumber(xsDataFile.path.value)
)
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF")
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
xsDataInputInterface.addImagePath(cbfFile)
else:
xsDataInputInterface.addImagePath(xsDataFile)
if self.xsDataFirstImage is None:
self.xsDataFirstImage = xsDataFile
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(
self.xsDataFirstImage, xsDataInputMXCuBE.getExperimentalCondition()
)
xsDataInputInterface.setExperimentalCondition(xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if self.edPluginControlInterface is not None:
self.connectProcess(self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(self.doFailureActionInterface)
def generateCommands(self, _xsDataInputH5ToCBF):
"""
This method creates a list of commands for H5ToXDS
"""
self.DEBUG("EDPluginH5ToCBFv1_0.generateCommands")
hdf5File = _xsDataInputH5ToCBF.hdf5File.path.value
directory = os.path.dirname(hdf5File)
prefix = EDUtilsImage.getPrefix(hdf5File)
imageNumber = _xsDataInputH5ToCBF.imageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
masterFile = os.path.join(
directory, prefix + "_{0}_master.h5".format(hdf5ImageNumber))
CBFFileName = prefix + "_%04d" % imageNumber + ".cbf"
tmpCBFFileName = "tmp_" + CBFFileName
if self.dataInput.forcedOutputDirectory is None:
self.CBFFile = os.path.join(directory, CBFFileName)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0o755)
self.CBFFile = os.path.join(forcedOutputDirectory, CBFFileName)
self.tmpCBFFile = os.path.join(self.getWorkingDirectory(),
tmpCBFFileName)
scriptCommandLine = "{0} {1} {2}".format(
masterFile, imageNumber - hdf5ImageNumber + 1, tmpCBFFileName)
return scriptCommandLine
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection(
)
if xsDataCollection is not None:
firstSubWedge = xsDataCollection.subWedge[0]
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataBeam = firstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self.fMinTransmission:
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "Please consider re-characterising with transmission set to 100 %"
self.page.font(_color="red", size="+2")
self.page.i()
self.page.h2(strWarningMessage1 + "<br>" +
strWarningMessage2)
self.page.i.close()
self.page.font.close()
self.page.h2("Data collection info")
firstImage = firstSubWedge.image[0]
strDate = firstImage.date.value
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
self.page.table(class_='dataCollectionInfo',
border_="1",
cellpadding_="0")
self.page.tr(align_="CENTER")
self.page.th("Data collection date",
bgcolor_=self.strTableColourTitle2)
self.page.th(strDate, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Image prefix", bgcolor_=self.strTableColourTitle2)
self.page.th(strPrefix, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Directory", bgcolor_=self.strTableColourTitle2)
self.page.th(strDirName, bgcolor_=self.strTableColourRows)
self.page.tr.close()
self.page.table.close()
def generateCommands(self, _xsDataInputH5ToCBF):
"""
This method creates a list of commands for H5ToXDS
"""
self.DEBUG("EDPluginH5ToCBFv1_0.generateCommands")
hdf5File = _xsDataInputH5ToCBF.hdf5File.path.value
directory = os.path.dirname(hdf5File)
prefix = EDUtilsImage.getPrefix(hdf5File)
imageNumber = _xsDataInputH5ToCBF.imageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
masterFile = os.path.join(directory, prefix + "_{0}_master.h5".format(hdf5ImageNumber))
CBFFileName = prefix + "_%04d" % imageNumber + ".cbf"
tmpCBFFileName = "tmp_" + CBFFileName
if self.dataInput.forcedOutputDirectory is None:
self.CBFFile = os.path.join(directory, CBFFileName)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0755)
self.CBFFile = os.path.join(forcedOutputDirectory, CBFFileName)
self.tmpCBFFile = os.path.join(self.getWorkingDirectory(), tmpCBFFileName)
scriptCommandLine = "{0} {1} {2}".format(masterFile, imageNumber - hdf5ImageNumber + 1, tmpCBFFileName)
return scriptCommandLine
def dataCollectionInfo(self):
xsDataCollection = self.xsDataResultCharacterisation.getDataCollection()
if xsDataCollection is not None:
firstSubWedge = xsDataCollection.subWedge[0]
# MXSUP-1445: Check if transmission is less than 10% and warn if it's the case
xsDataBeam = firstSubWedge.getExperimentalCondition().getBeam()
if xsDataBeam.getTransmission() is not None:
fTransmission = xsDataBeam.getTransmission().getValue()
if fTransmission < self.fMinTransmission:
strWarningMessage1 = "WARNING! Transmission for characterisation set to %.1f %%" % fTransmission
strWarningMessage2 = "If this transmission setting is not intentional, please consider re-characterising with transmission set to 100 %"
self.workflowStepReport.addWarning(strWarningMessage1)
self.workflowStepReport.addWarning(strWarningMessage2)
firstImage = firstSubWedge.image[0]
if firstImage.date is not None:
strDate = firstImage.date.value
else:
strDate = "-----"
strPrefix = EDUtilsImage.getPrefix(firstImage.path.value)
strDirName = os.path.dirname(firstImage.path.value)
dictTable = {"type": "table",
"title": "Data collection info",
"columns": [],
"data": []}
listRow = []
dictTable["columns"].append("Data collection date")
listRow.append(strDate)
dictTable["columns"].append("Image prefix")
listRow.append(strPrefix)
dictTable["columns"].append("Directory")
listRow.append(strDirName)
dictTable["data"].append(listRow)
#
self.workflowStepReport.addTable("Data collection info",
dictTable["columns"],
dictTable["data"],
orientation="vertical")
def createImageDict(self, _xsDataControlDozorInput):
# Create dictionary of all images with the image number as key
dictImage = {}
if len(_xsDataControlDozorInput.image) > 0:
listImage = _xsDataControlDozorInput.image
pathToFirstImage = listImage[0].path.value
self.directory = os.path.dirname(pathToFirstImage)
self.template = os.path.basename(pathToFirstImage).replace("0001", "####")
else:
# Create list of images
listImage = []
self.directory = _xsDataControlDozorInput.directory.path.value
self.template = _xsDataControlDozorInput.template.value
startNo = _xsDataControlDozorInput.startNo.value
endNo = _xsDataControlDozorInput.endNo.value
for imageIndex in range(startNo, endNo + 1):
imageName = self.template % imageIndex
imagePath = os.path.join(self.directory, imageName)
listImage.append(XSDataFile(XSDataString(imagePath)))
for image in listImage:
imagePath = image.path.value
imageNo = EDUtilsImage.getImageNumber(imagePath)
dictImage[imageNo] = image
return dictImage
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_0.process")
xsDataResultControlDozor = XSDataResultControlDozor()
# Check if connection to ISPyB needed
if self.dataInput.dataCollectionId is not None:
edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = edPluginRetrieveDataCollection.dataOutput.dataCollection
batchSize = ispybDataCollection.numberOfImages
if batchSize > self.maxBatchSize:
batchSize = self.maxBatchSize
if abs(ispybDataCollection.overlap) > 1:
self.hasOverlap = True
self.overlap = ispybDataCollection.overlap
dictImage = self.createImageDictFromISPyB(ispybDataCollection)
else:
# No connection to ISPyB, take parameters from input
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
dictImage = self.createImageDict(self.dataInput)
listAllBatches = self.createListOfBatches(dictImage.keys(), batchSize)
if dictImage[listAllBatches[0][0]].path.value.endswith("h5"):
# Convert HDF5 images to CBF
self.cbfTempDir = tempfile.mkdtemp(prefix="CbfTemp_")
dictImage, self.hasHdf5Prefix = self.convertToCBF(dictImage)
for listBatch in listAllBatches:
# Read the header from the first image in the batch
xsDataFile = dictImage[listBatch[0]]
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataInteger(3)
xsDataInputDozor.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputDozor.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
xsDataInputDozor.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputDozor.imageStep : XSDataDouble optional
xsDataInputDozor.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputDozor.firstImageNumber = subWedge.image[0].number
xsDataInputDozor.numberImages = XSDataInteger(len(listBatch))
if self.hasOverlap:
xsDataInputDozor.overlap = XSDataAngle(self.overlap)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
if EDUtilsPath.isEMBL():
strXDSTemplate = "%s_?????.%s" % (strPrefix, strSuffix)
elif self.hasHdf5Prefix and not self.hasOverlap:
strXDSTemplate = "%s_??????.%s" % (strPrefix, strSuffix)
else:
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputDozor.nameTemplateImage = XSDataString(
os.path.join(os.path.dirname(strFileName), strXDSTemplate)
)
xsDataInputDozor.wedgeNumber = self.dataInput.wedgeNumber
xsDataInputDozor.radiationDamage = self.dataInput.radiationDamage
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor_%05d" % subWedge.image[0].number.value)
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.executeSynchronous()
indexImage = 0
for xsDataResultDozor in edPluginDozor.dataOutput.imageDozor:
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.number = xsDataResultDozor.number
xsDataControlImageDozor.image = dictImage[listBatch[indexImage]]
xsDataControlImageDozor.spotsNumOf = xsDataResultDozor.spotsNumOf
xsDataControlImageDozor.spotsIntAver = xsDataResultDozor.spotsIntAver
xsDataControlImageDozor.spotsResolution = xsDataResultDozor.spotsResolution
xsDataControlImageDozor.powderWilsonScale = xsDataResultDozor.powderWilsonScale
xsDataControlImageDozor.powderWilsonBfactor = xsDataResultDozor.powderWilsonBfactor
xsDataControlImageDozor.powderWilsonResolution = xsDataResultDozor.powderWilsonResolution
xsDataControlImageDozor.powderWilsonCorrelation = xsDataResultDozor.powderWilsonCorrelation
xsDataControlImageDozor.powderWilsonRfactor = xsDataResultDozor.powderWilsonRfactor
xsDataControlImageDozor.mainScore = xsDataResultDozor.mainScore
xsDataControlImageDozor.spotScore = xsDataResultDozor.spotScore
xsDataControlImageDozor.visibleResolution = xsDataResultDozor.visibleResolution
xsDataControlImageDozor.spotFile = xsDataResultDozor.spotFile
xsDataControlImageDozor.angle = xsDataResultDozor.angle
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
if xsDataResultControlDozor.inputDozor is None:
xsDataResultControlDozor.inputDozor = XSDataDozorInput().parseString(xsDataInputDozor.marshal())
indexImage += 1
xsDataResultControlDozor.halfDoseTime = edPluginDozor.dataOutput.halfDoseTime
self.dataOutput = xsDataResultControlDozor
if self.cbfTempDir is not None:
shutil.rmtree(self.cbfTempDir)
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_1.process")
msg = "EDPluginControlDozorXmlRpcv1_0 started..."
self.sendMessageToMXCuBE("Processing started...", "info")
xsDataResultControlDozor = XSDataResultControlDozor()
firstFileName = self.dataInput.template.value % (
self.dataInput.first_run_number.value,
self.dataInput.first_image_number.value)
fWaitFileTimeout = 180 #sec
self.waitFileFirst = self.loadPlugin("EDPluginMXWaitFilev1_1",
"MXWaitFileFirst")
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(
XSDataString(firstFileName))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.waitFileFirst.size = XSDataInteger(1000000)
self.waitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.waitFileFirst.executeSynchronous()
if self.waitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (
fWaitFileTimeout, firstFileName)
#self.addWarningMessage(strWarningMessage)
#self.WARNING(strWarningMessage)
#self.sendMessageToMXCuBE(strWarningMessage, "error")
edPluginControlReadImageHeader = self.loadPlugin(
self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = XSDataFile(
XSDataString(firstFileName))
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataDouble(3.0)
xsDataInputDozor.detectorDistance = XSDataDouble(
detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
# GB: the 50 might need tunig to CPU speed and number of. 2000 is a current limit of Dozor.
self.maxChunkSize = 4000 #a min (150 * 2527 * 2463 /detector.numberPixelX.value / detector.numberPixelY.value, 2000)
_beamstop = self.beamstop(detector)
if _beamstop is not None:
#self.WARNING("Setting beamstop shadow: %s"%_beamstop)
xsDataInputDozor.ixMin = XSDataInteger(_beamstop['ix_min'])
xsDataInputDozor.iyMin = XSDataInteger(_beamstop['iy_min'])
xsDataInputDozor.ixMax = XSDataInteger(_beamstop['ix_max'])
xsDataInputDozor.iyMax = XSDataInteger(_beamstop['iy_max'])
if self.dataInput.pixelMin is not None:
xsDataInputDozor.pixelMin = self.dataInput.pixelMin
if self.dataInput.pixelMax is not None:
xsDataInputDozor.pixelMax = self.dataInput.pixelMax
_serial = 0
_startTime = time.time()
chunk_list = self.schedule(goniostat.rotationAxisStart.value,
goniostat.oscillationWidth.value)
for chunk in chunk_list:
if not self.poll_file(
self.dataInput.template.value %
(chunk['run_number'], chunk['first'] + chunk['number_of'] - 1),
(beam.exposureTime.value + 0.003) * chunk['number_of'] + 30):
self.sendMessageToMXCuBE("Timeout waiting for frame: %d" %
(chunk['first'] + chunk['number_of']),
level="error")
return
xsDataInputDozor.oscillationRange = XSDataDouble(
chunk['rotation_range'])
xsDataInputDozor.startingAngle = XSDataDouble(
chunk['rotation_start'])
xsDataInputDozor.firstImageNumber = XSDataInteger(chunk['first'])
xsDataInputDozor.numberImages = XSDataInteger(chunk['number_of'])
strFileName = self.dataInput.template.value % (chunk['run_number'],
chunk['first'])
strXDSTemplate = EDUtilsImage.getTemplate(strFileName, '?')
xsDataInputDozor.nameTemplateImage = XSDataString(
os.path.join(os.path.dirname(strFileName), strXDSTemplate))
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor")
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.executeSynchronous()
xsDataChunkResultControlImageDozor = XSDataResultControlDozor()
dozor_batch_list = [] #[[1,4,3,8,6],
#[2, 5, 3, 3, 7],[1, 3, 12, 11, 4],[4, 2, 3, 5, 7]]
#ozor_image_dict = {}
diff_image_count = 0
xsDataControlImageDozor = XSDataControlImageDozor()
for xsDataResultDozor in edPluginDozor.dataOutput.imageDozor:
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.number = xsDataResultDozor.number
strFileName = self.dataInput.template.value % (
chunk['run_number'], xsDataControlImageDozor.number.value)
xsDataControlImageDozor.image = XSDataFile(
XSDataString(strFileName))
xsDataControlImageDozor.spots_num_of = xsDataResultDozor.spots_num_of
xsDataControlImageDozor.spots_int_aver = xsDataResultDozor.spots_int_aver
xsDataControlImageDozor.spots_resolution = xsDataResultDozor.spots_resolution
xsDataControlImageDozor.powder_wilson_scale = xsDataResultDozor.powder_wilson_scale
xsDataControlImageDozor.powder_wilson_bfactor = xsDataResultDozor.powder_wilson_bfactor
xsDataControlImageDozor.powder_wilson_resolution = xsDataResultDozor.powder_wilson_resolution
xsDataControlImageDozor.powder_wilson_correlation = xsDataResultDozor.powder_wilson_correlation
xsDataControlImageDozor.powder_wilson_rfactor = xsDataResultDozor.powder_wilson_rfactor
xsDataControlImageDozor.score = xsDataResultDozor.score
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
dozor_batch_list.append(
(xsDataControlImageDozor.number.getValue(),
xsDataControlImageDozor.spots_num_of.getValue(),
xsDataControlImageDozor.spots_int_aver.getValue(),
xsDataControlImageDozor.spots_resolution.getValue(),
xsDataControlImageDozor.score.getValue()))
if xsDataControlImageDozor.spots_num_of.getValue() > 0:
diff_image_count += 1
xsDataChunkResultControlImageDozor.addImageDozor(
xsDataControlImageDozor)
xsDataChunkResultControlImageDozor.exportToFile(
"ResultControlDozor_Chunk_%06d.xml" % _serial)
self.sendResultToMXCuBE(dozor_batch_list)
_serial += 1
self.screen("Chunk %d/%d done in %.3f seconds" % \
(_serial, len(chunk_list), time.time()-_startTime))
self.sendMessageToMXCuBE("Chunk %d/%d done in %.2f sec., num diffr. frames: %d/%d" % \
(_serial,
len(chunk_list),
time.time() - _startTime,
diff_image_count,
len(dozor_batch_list)
)
)
_startTime = time.time()
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlInterfaceToMXCuBEv1_4.process...")
xsDataInputMXCuBE = self.getDataInput()
xsDataInputInterface = XSDataInputInterface()
self.edPluginControlInterface = self.loadPlugin(self.strPluginControlInterface)
self.xsDataFirstImage = None
for xsDataSetMXCuBE in xsDataInputMXCuBE.getDataSet():
for xsDataFile in xsDataSetMXCuBE.getImageFile():
if xsDataFile.path.value.endswith(".h5"):
self.bIsEigerDetector = True
self.xsDataFirstImage = xsDataFile
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(xsDataFile.path)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(EDUtilsImage.getImageNumber(xsDataFile.path.value))
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF")
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
xsDataInputInterface.addImagePath(cbfFile)
else:
xsDataInputInterface.addImagePath(xsDataFile)
if self.xsDataFirstImage is None:
self.xsDataFirstImage = xsDataFile
# Check that images are on disk, otherwise wait
for xsDataImagePath in xsDataInputInterface.imagePath:
imagePath = xsDataImagePath.path.value
if os.path.exists(imagePath):
message = "Input file ok: {0}".format(imagePath)
self.screen(message)
self.sendMessageToMXCuBE(message)
else:
self.sendMessageToMXCuBE("Waiting for file: {0}, timeout {1} s".format(imagePath, self.fMXWaitFileTimeOut))
edPluginMXWaitFile = self.loadPlugin(self.strPluginMXWaitFileName)
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
xsDataInputMXWaitFile.file = XSDataFile(XSDataString(imagePath))
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setTimeOut(XSDataTime(self.fMXWaitFileTimeOut))
self.DEBUG("Wait file timeOut set to %f" % self.fMXWaitFileTimeOut)
edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
edPluginMXWaitFile.executeSynchronous()
if edPluginMXWaitFile.dataOutput.timedOut.value:
errorMessage = "ERROR! File {0} does not exist on disk.".format(imagePath)
self.ERROR(errorMessage)
self.sendMessageToMXCuBE(errorMessage, "error")
self.setFailure()
break
xsDataExperimentalCondition = self.getFluxAndBeamSizeFromISPyB(self.xsDataFirstImage, \
xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputInterface.setExperimentalCondition(xsDataExperimentalCondition)
xsDataInputInterface.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputInterface.setSample(xsDataInputMXCuBE.getSample())
xsDataInputInterface.setDataCollectionId(xsDataInputMXCuBE.getDataCollectionId())
self.edPluginControlInterface.setDataInput(xsDataInputInterface)
if not self.isFailure() and self.edPluginControlInterface is not None:
self.connectProcess(self.edPluginControlInterface.executeSynchronous)
self.edPluginControlInterface.connectSUCCESS(self.doSuccessActionInterface)
self.edPluginControlInterface.connectFAILURE(self.doFailureActionInterface)
def generateXSDataMOSFLMInputIndexing(_xsDataIndexingInput):
"""
Translation from XSDataIndexingInput to XSDataMOSFLMInputIndexing.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing")
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataExperimentalCondition = _xsDataIndexingInput.getExperimentalCondition(
)
xsDataCrystal = _xsDataIndexingInput.getCrystal()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
if (xsDataExperimentalCondition is None):
xsDataExperimentalCondition = xsDataSubWedgeList[
0].getExperimentalCondition()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(dBeamPositionX))
xsDataMOSFLMBeamPosition.setY(XSDataLength(dBeamPositionY))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(dWavelength))
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(dDistance))
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
strPath = xsDataImageFirst.getPath().getValue()
strFileName = os.path.basename(strPath)
strDirectory = os.path.dirname(strPath)
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFileName, 1)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFileName, "#")
xsDataMOSFLMInputIndexing.setTemplate(XSDataString(strMOSFLMTemplate))
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(strDirectory))
if (xsDataCrystal is not None):
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
xsDataStringName = xsDataSpaceGroup.getName()
if (xsDataStringName is not None):
xsDataMOSFLMInputIndexing.setSymmetry(
XSDataString(xsDataStringName.getValue()))
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth(
).getValue()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
for xsDataImage in xsDataImageList:
# Create the MOSFLM image object
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fImageOscillationStart = fGonioStatOscillationStart + (
iImageNumber -
iLowestImageNumber) * fGonioStatOscillationRange
xsDataMOSFLMImage.setRotationAxisStart(
XSDataAngle(fImageOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fImageOscillationStart +
fGonioStatOscillationRange))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputIndexing
def generateXSDataMOSFLMInputGeneratePrediction(
xsDataGeneratePredictionInput):
"""
Translation from XSDataGeneratePredictionInput to XSDataMOSFLMInputGeneratePrediction.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction"
)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataIndexingSolutionSelected = xsDataGeneratePredictionInput.getSelectedIndexingSolution(
)
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined(
)
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction(
)
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputGeneratePrediction.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setMosaicity(
xsDataCrystal.getMosaicity())
xsDataMOSFLMInputGeneratePrediction.setSymmetry(
xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
xsDataMOSFLMInputGeneratePrediction.setWavelength(
xsDataBeam.getWavelength())
xsDataMOSFLMInputGeneratePrediction.setDistance(
xsDataDetector.getDistance())
xsDataMOSFLMInputGeneratePrediction.setDirectory(
XSDataString(strDirectoryFirst))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
# The MOSFLM plugin can only handle one image
xsDataImage = xsDataSubWedge.getImage()[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
iImageNumber = xsDataImage.getNumber().getValue()
if xsDataDetector.type.value == "eiger2_16m":
strMOSFLMTemplate = EDUtilsImage.getH5MasterTemplate(
strFilenameFirst, iImageNumber)
else:
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputGeneratePrediction.setTemplate(
XSDataString(strMOSFLMTemplate))
xsDataMOSFLMImage = XSDataMOSFLMImage()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(
XSDataAngle(fOscillationStart + fOscillationRange))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputGeneratePrediction
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlDozorv1_0.process")
self.sendMessageToMXCuBE("Processing started...", "info")
EDUtilsParallel.initializeNbThread()
xsDataResultControlDozor = XSDataResultControlDozor()
# Check if connection to ISPyB needed
if self.dataInput.dataCollectionId is not None:
edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = edPluginRetrieveDataCollection.dataOutput.dataCollection
if self.batchSize is None:
batchSize = ispybDataCollection.numberOfImages
else:
batchSize = self.batchSize
if batchSize > self.maxBatchSize:
batchSize = self.maxBatchSize
if abs(ispybDataCollection.overlap) > 1:
self.hasOverlap = True
self.overlap = ispybDataCollection.overlap
dictImage = self.createImageDictFromISPyB(ispybDataCollection)
else:
# No connection to ISPyB, take parameters from input
if self.dataInput.batchSize is None:
batchSize = self.maxBatchSize
else:
batchSize = self.dataInput.batchSize.value
dictImage = self.createImageDict(self.dataInput)
self.screen("Dozor batch size: {0}".format(batchSize))
if self.dataInput.hdf5BatchSize is not None:
self.hdf5BatchSize = self.dataInput.hdf5BatchSize.value
listAllBatches = self.createListOfBatches(dictImage.keys(), batchSize)
if dictImage[listAllBatches[0][0]].path.value.endswith("h5"):
# Convert HDF5 images to CBF
self.screen("HDF5 converter batch size: {0}".format(self.batchSize))
if self.doRadiationDamage:
self.cbfTempDir = None
else:
self.cbfTempDir = tempfile.mkdtemp(prefix="CbfTemp_")
listHdf5Batches = self.createListOfBatches(dictImage.keys(), self.batchSize)
dictImage, self.hasHdf5Prefix = self.convertToCBF(dictImage, listHdf5Batches, self.doRadiationDamage)
for listBatch in listAllBatches:
# Read the header from the first image in the batch
xsDataFile = dictImage[listBatch[0]]
edPluginControlReadImageHeader = self.loadPlugin(self.strEDPluginControlReadImageHeaderName)
xsDataInputReadImageHeader = XSDataInputReadImageHeader()
xsDataInputReadImageHeader.image = xsDataFile
edPluginControlReadImageHeader.dataInput = xsDataInputReadImageHeader
edPluginControlReadImageHeader.executeSynchronous()
subWedge = edPluginControlReadImageHeader.dataOutput.subWedge
xsDataInputDozor = XSDataInputDozor()
beam = subWedge.experimentalCondition.beam
detector = subWedge.experimentalCondition.detector
goniostat = subWedge.experimentalCondition.goniostat
xsDataInputDozor.detectorType = detector.type
xsDataInputDozor.exposureTime = XSDataDouble(beam.exposureTime.value)
xsDataInputDozor.spotSize = XSDataInteger(3)
xsDataInputDozor.detectorDistance = XSDataDouble(detector.distance.value)
xsDataInputDozor.wavelength = XSDataDouble(beam.wavelength.value)
# xsDataInputDozor.fractionPolatization : XSDataDouble optional
orgx = detector.beamPositionY.value / detector.pixelSizeY.value
orgy = detector.beamPositionX.value / detector.pixelSizeX.value
xsDataInputDozor.orgx = XSDataDouble(orgx)
xsDataInputDozor.orgy = XSDataDouble(orgy)
xsDataInputDozor.oscillationRange = XSDataDouble(goniostat.oscillationWidth.value)
# xsDataInputDozor.imageStep : XSDataDouble optional
xsDataInputDozor.startingAngle = XSDataDouble(goniostat.rotationAxisStart.value)
xsDataInputDozor.firstImageNumber = subWedge.image[0].number
xsDataInputDozor.numberImages = XSDataInteger(len(listBatch))
if self.hasOverlap:
xsDataInputDozor.overlap = XSDataAngle(self.overlap)
strFileName = subWedge.image[0].path.value
strPrefix = EDUtilsImage.getPrefix(strFileName)
strSuffix = EDUtilsImage.getSuffix(strFileName)
if EDUtilsPath.isEMBL():
strXDSTemplate = "%s_?????.%s" % (strPrefix, strSuffix)
elif self.hasHdf5Prefix and not self.hasOverlap:
strXDSTemplate = "%s_??????.%s" % (strPrefix, strSuffix)
else:
strXDSTemplate = "%s_????.%s" % (strPrefix, strSuffix)
xsDataInputDozor.nameTemplateImage = XSDataString(os.path.join(os.path.dirname(strFileName), strXDSTemplate))
xsDataInputDozor.wedgeNumber = self.dataInput.wedgeNumber
xsDataInputDozor.radiationDamage = self.dataInput.radiationDamage
edPluginDozor = self.loadPlugin(self.strEDPluginDozorName, "Dozor_%05d" % subWedge.image[0].number.value)
edPluginDozor.dataInput = xsDataInputDozor
edPluginDozor.execute()
edPluginDozor.synchronize()
indexImage = 0
imageDozorBatchList = []
for xsDataResultDozor in edPluginDozor.dataOutput.imageDozor:
xsDataControlImageDozor = XSDataControlImageDozor()
xsDataControlImageDozor.number = xsDataResultDozor.number
xsDataControlImageDozor.image = dictImage[listBatch[indexImage]]
xsDataControlImageDozor.spotsNumOf = xsDataResultDozor.spotsNumOf
xsDataControlImageDozor.spotsIntAver = xsDataResultDozor.spotsIntAver
xsDataControlImageDozor.spotsResolution = xsDataResultDozor.spotsResolution
xsDataControlImageDozor.powderWilsonScale = xsDataResultDozor.powderWilsonScale
xsDataControlImageDozor.powderWilsonBfactor = xsDataResultDozor.powderWilsonBfactor
xsDataControlImageDozor.powderWilsonResolution = xsDataResultDozor.powderWilsonResolution
xsDataControlImageDozor.powderWilsonCorrelation = xsDataResultDozor.powderWilsonCorrelation
xsDataControlImageDozor.powderWilsonRfactor = xsDataResultDozor.powderWilsonRfactor
xsDataControlImageDozor.mainScore = xsDataResultDozor.mainScore
xsDataControlImageDozor.spotScore = xsDataResultDozor.spotScore
xsDataControlImageDozor.visibleResolution = xsDataResultDozor.visibleResolution
xsDataControlImageDozor.spotFile = xsDataResultDozor.spotFile
xsDataControlImageDozor.angle = xsDataResultDozor.angle
xsDataResultControlDozor.addImageDozor(xsDataControlImageDozor)
if xsDataResultControlDozor.inputDozor is None:
xsDataResultControlDozor.inputDozor = XSDataDozorInput().parseString(xsDataInputDozor.marshal())
indexImage += 1
dozorSpotListShape = []
dozorSpotList = []
spotFile = None
if xsDataControlImageDozor.spotFile is not None:
spotFile = xsDataControlImageDozor.spotFile.path.value
if os.path.exists(spotFile):
numpyArray = numpy.loadtxt(spotFile, skiprows=3)
dozorSpotList = base64.b64encode(numpyArray.tostring())
dozorSpotListShape.append(numpyArray.shape[0])
if len(numpyArray.shape) > 1:
dozorSpotListShape.append(numpyArray.shape[1])
imageDozorDict = {"index": xsDataControlImageDozor.number.value,
"imageName": xsDataControlImageDozor.image.path.value,
"dozor_score": xsDataControlImageDozor.mainScore.value,
"dozorSpotsNumOf" : xsDataControlImageDozor.spotsNumOf.value,
"dozorSpotFile": spotFile,
"dozorSpotList" : dozorSpotList,
"dozorSpotListShape": dozorSpotListShape,
"dozorSpotsIntAver": xsDataControlImageDozor.spotsIntAver.value,
"dozorSpotsResolution": xsDataControlImageDozor.spotsResolution.value
}
imageDozorBatchList.append(imageDozorDict)
xsDataResultControlDozor.halfDoseTime = edPluginDozor.dataOutput.halfDoseTime
xsDataResultControlDozor.pngPlots = edPluginDozor.dataOutput.pngPlots
self.sendResultToMXCuBE(imageDozorBatchList)
self.sendMessageToMXCuBE("Batch processed")
self.dataOutput = xsDataResultControlDozor
if self.cbfTempDir is not None:
if self.dataInput.keepCbfTmpDirectory is not None and self.dataInput.keepCbfTmpDirectory.value:
self.dataOutput.pathToCbfDirectory = XSDataFile(XSDataString(self.cbfTempDir))
else:
shutil.rmtree(self.cbfTempDir)
def generateDataCollectionDescriptorForSubWedge(self, calibDate, omegaR, kappaR, phiR, beamD, polarisationP, exposuretime, imagewidth, numberimages, wavelength, OmegaV, KappaV, PhiV, imgFnames):
##CONTAINER
self.xsDC_v2 = XSDataCollection_v2()
##GonioCalib
calib = XSDataMXv2.XSCalibration()
cdate = XSDataMXv2.XSDataDate()
cdate.setValue(XSDataMXv2.XSDataString(calibDate))
calib.setDate(cdate)
#OmegaCalib
omegacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(omegaR[0])
zdir.setV2(omegaR[1])
zdir.setV3(omegaR[2])
omegacal.setZerodirection(zdir)
omegacal.setXSCalibration(calib)
#KappaCalib
kappacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(kappaR[0])
zdir.setV2(kappaR[1])
zdir.setV3(kappaR[2])
kappacal.setZerodirection(zdir)
kappacal.setXSCalibration(calib)
#PhiCalib
phical = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(phiR[0])
zdir.setV2(phiR[1])
zdir.setV3(phiR[2])
phical.setZerodirection(zdir)
phical.setXSCalibration(calib)
##goni
actgonio = XSDataMXv2.XSRotationalGoniostat()
#omega
omega = XSDataMXv2.XSGoniostatBaseAxis()
omega.setName(XSDataMXv2.XSDataString('Omega'))
omega.setIsscannable(XSDataMXv2.XSDataBoolean(1))
omega.addXSCalibratedDisplacementAxis(omegacal)
actgonio.setXSGoniostatBaseAxis(omega)
#kappa
kappa = XSDataMXv2.XSGoniostatRotatableAxis()
kappa.setName(XSDataMXv2.XSDataString('Kappa'))
kappa.setIsscannable(XSDataMXv2.XSDataBoolean(0))
kappa.addXSCalibratedDisplacementAxis(kappacal)
actgonio.addXSGoniostatRotatableAxis(kappa)
#phi
phi = XSDataMXv2.XSGoniostatRotatableAxis()
phi.setName(XSDataMXv2.XSDataString('Phi'))
phi.setIsscannable(XSDataMXv2.XSDataBoolean(0))
phi.addXSCalibratedDisplacementAxis(phical)
actgonio.addXSGoniostatRotatableAxis(phi)
##beam
beam = XSDataMXv2.XSBeam()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(polarisationP[0])
zdir.setV2(polarisationP[1])
zdir.setV3(polarisationP[2])
beam.setPolarisatation(zdir)
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(beamD[0])
zdir.setV2(beamD[1])
zdir.setV3(beamD[2])
beam.setDirection(zdir)
##detector
detector = XSDataMXv2.XSDetector()
detector.setName(XSDataMXv2.XSDataString('detector'))
###detector.set
##SUBWEDGE
sw = XSSubWedge_v2()
# template
sw.setImagefilenametemplate(XSDataMXv2.XSDataString(EDUtilsImage.getTemplate(imgFnames[0], "#")))
# images
for imgFname in imgFnames:
img = XSDiffractionImages_v2()
img.setFilename(XSDataMXv2.XSDataString(imgFname))
sw.addXSDiffractionImages(img)
#RotationExposure
rotexp = XSRotationExposure_v2()
rotexp.setExposuretime(XSDataMXv2.XSDataTime(exposuretime))
rotexp.setImagewidth(XSDataMXv2.XSDataAngle(imagewidth))
rotexp.setNumberimages(XSDataMXv2.XSDataInteger(numberimages))
rotexp.setXSGoniostatAxis(omega)
sw.setXSRotationExposure(rotexp)
#Beamsetting
beams = XSBeamSetting_v2()
w = XSDataMXv2.XSDataWavelength()
w.setValue(wavelength)
beams.setWavelength(w)
beams.setXSBeam(beam)
sw.setXSBeamSetting(beams)
#RotationalGonioSetting
rotgset = XSDataMXv2.XSRotationalGoniostatSetting()
rotgset.setXSRotationalGoniostat(actgonio)
oang = XSDataMXv2.XSDataAngle()
oang.setValue(OmegaV)
rotgset.setBaseaxissetting(oang)
kang = XSDataMXv2.XSDataAngle()
kang.setValue(KappaV)
rotgset.addAxissetting(kang)
pang = XSDataMXv2.XSDataAngle()
pang.setValue(PhiV)
rotgset.addAxissetting(pang)
sw.setXSRotationalGoniostatSetting(rotgset)
#DetectorSetting TODOTODO
detset = XSDataMXv2.XSDetectorSetting()
#axissetting=(XSDataMXv2.XSDataAngle().setValue(KappaV),XSDataMXv2.XSDataAngle().setValue(PhiV))
#detset.setAxissetting(axissetting)
self.xsDC_v2.addXSSubWedge(sw)
imgFname = self.xsDataResultSubWedgeAssemble.getSubWedge()[0].getImage()[0].getPath().getValue()
self.xsDC_v2.outputFile(os.path.dirname(imgFname) + '/edna_' + EDUtilsImage.getTemplate(imgFname, "#") + '_auto')
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
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictMARCCDHeader = self.readHeaderMarccd(strPath)
if (dictMARCCDHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = int(dictMARCCDHeader["nslow"])
iNoPixelsY = int(dictMARCCDHeader["nfast"])
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
fPixelSizeX = float(dictMARCCDHeader["pixelsize_x"]) / 1000.0
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(dictMARCCDHeader["pixelsize_y"]) / 1000.0
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
fBeamPositionX = float(dictMARCCDHeader["beam_x"]) / 1000.0
fBeamPositionY = float(dictMARCCDHeader["beam_y"]) / 1000.0
# Fix for bug 397 - check if the beam position is close to the centre of the image
fTwoTheta = float(dictMARCCDHeader["end_twotheta"]) / 1000.0
xsDataDetector.setTwoTheta(XSDataAngle(fTwoTheta))
if (abs(fTwoTheta) < 0.1):
if (abs(fBeamPositionX /
(fPixelSizeX / 1000.0) - iNoPixelsX / 2.0) >
(2 * iNoPixelsX)):
fBeamPositionX = fBeamPositionX * fPixelSizeX / 1000.0
fBeamPositionY = fBeamPositionY * fPixelSizeY / 1000.0
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictMARCCDHeader["xtal_to_detector"]) / 1000.0
if (abs(fDistance) < 0.1):
fDistanceStart = float(
dictMARCCDHeader["start_xtal_to_detector"]) / 1000.0
fDistanceEnd = float(
dictMARCCDHeader["end_xtal_to_detector"]) / 1000.0
if (abs(fDistanceStart - fDistanceEnd) < 0.1):
fDistance = fDistanceStart
else:
# Somethings very wrong with the distances...
strErrorMessage = "EDPluginExecReadImageHeaderMARCCDv10.process : Inconsistency in MAR CCD image header: start_xtal_to_detector = %d, end_xtal_to_detector = %d" % \
(fDistanceStart, fDistanceEnd)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataDetector.setDistance(XSDataLength(fDistance))
xsDataDetector.setNumberBytesInHeader(
XSDataInteger(float(dictMARCCDHeader["header_size"])))
#xsDataDetector.setSerialNumber( XSDataInteger( dictMARCCDHeader[ "DETECTOR_SN" ] ) ) )
#xsDataDetector.setBin( XSDataString( dictMARCCDHeader[ "BIN" ] ) ) )
#xsDataDetector.setDataType( XSDataString( dictMARCCDHeader[ "TYPE" ] ) ) )
#xsDataDetector.setByteOrder( XSDataString( dictMARCCDHeader[ "BYTE_ORDER" ] ) ) )
xsDataDetector.setImageSaturation(
XSDataInteger(int(dictMARCCDHeader["saturation_level"])))
# Determine type of detector...
if (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("MAR CCD 165"))
xsDataDetector.setType(XSDataString("mar165"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("MAR CCD 225"))
xsDataDetector.setType(XSDataString("mar225"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("MAR CCD 325"))
xsDataDetector.setType(XSDataString("mar325"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % (
"EDPluginExecReadImageHeaderMARCCDv10.process",
"Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(
XSDataWavelength(
float(dictMARCCDHeader["source_wavelength"]) / 100000.0))
xsDataBeam.setExposureTime(
XSDataTime(float(dictMARCCDHeader["exposure_time"]) / 1000.0))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictMARCCDHeader["start_phi"]) / 1000.0
fOscillationWidth = float(
dictMARCCDHeader["rotation_range"]) / 1000.0
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))
strTimeStamp = dictMARCCDHeader["acquire_timestamp"]
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 process(self, _edObject=None):
EDPluginExec.process(self)
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictEiger4MHeader = self.readHeaderEiger4M(strPath)
if (dictEiger4MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderEiger4Mv10.process : Cannot read header : %s" % strPath
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 2070
iNoPixelsY = 2167
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictEiger4MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictEiger4MHeader["Beam_xy"].replace("(", " ").replace(")", " ").replace(",", " ").split()
fBeamPositionX = float(listBeamPosition[1]) * fPixelSizeX
fBeamPositionY = float(listBeamPosition[0]) * fPixelSizeY
xsDataDetector.setBeamPositionX(XSDataLength(fBeamPositionX))
xsDataDetector.setBeamPositionY(XSDataLength(fBeamPositionY))
fDistance = float(dictEiger4MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictEiger4MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictEiger4MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictEiger4MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictEiger4MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictEiger4MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictEiger4MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("EIGER 4M"))
xsDataDetector.setType(XSDataString("eiger4m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictEiger4MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictEiger4MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictEiger4MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictEiger4MHeader[ "Angle_increment" ].split(" ")[0])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
#
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strPath))
if "DateTime" in dictEiger4MHeader:
strTimeStamp = dictEiger4MHeader[ "DateTime" ]
xsDataImage.setDate(XSDataString(strTimeStamp))
iImageNumber = EDUtilsImage.getImageNumber(strPath)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def generateXSDataMOSFLMInputGeneratePrediction(xsDataGeneratePredictionInput):
"""
Translation from XSDataGeneratePredictionInput to XSDataMOSFLMInputGeneratePrediction.
"""
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputGeneratePrediction")
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
from XSDataMOSFLMv10 import XSDataMOSFLMInputGeneratePrediction
xsDataIndexingSolutionSelected = xsDataGeneratePredictionInput.getSelectedIndexingSolution()
xsDataCollection = xsDataGeneratePredictionInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputGeneratePrediction = XSDataMOSFLMInputGeneratePrediction()
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputGeneratePrediction.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputGeneratePrediction.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputGeneratePrediction.setMosaicity(xsDataCrystal.getMosaicity())
xsDataMOSFLMInputGeneratePrediction.setSymmetry(xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
xsDataMOSFLMInputGeneratePrediction.setWavelength(xsDataBeam.getWavelength())
xsDataMOSFLMInputGeneratePrediction.setDistance(xsDataDetector.getDistance())
xsDataMOSFLMInputGeneratePrediction.setDirectory(XSDataString(strDirectoryFirst))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(xsDataDetector)
xsDataMOSFLMInputGeneratePrediction.setDetector(xsDataMOSFLMDetector)
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputGeneratePrediction.setTemplate(XSDataString(strMOSFLMTemplate))
# The MOSFLM plugin can only handle one image
xsDataImage = xsDataSubWedge.getImage()[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(XSDataAngle(fOscillationStart + fOscillationRange))
xsDataMOSFLMInputGeneratePrediction.setImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputGeneratePrediction
def generateXSDataMOSFLMInputIndexing(_xsDataIndexingInput):
"""
Translation from XSDataIndexingInput to XSDataMOSFLMInputIndexing.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIndexing
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMImage
EDVerbose.DEBUG("EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIndexing")
xsDataCollection = _xsDataIndexingInput.getDataCollection()
xsDataExperimentalCondition = _xsDataIndexingInput.getExperimentalCondition()
xsDataCrystal = _xsDataIndexingInput.getCrystal()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataMOSFLMInputIndexing = XSDataMOSFLMInputIndexing()
if (xsDataExperimentalCondition is None):
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
dWavelength = xsDataBeam.getWavelength().getValue()
dDistance = xsDataDetector.getDistance().getValue()
dBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
dBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(XSDataLength(dBeamPositionX))
xsDataMOSFLMBeamPosition.setY(XSDataLength(dBeamPositionY))
xsDataMOSFLMInputIndexing.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(xsDataDetector)
xsDataMOSFLMInputIndexing.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInputIndexing.setWavelength(XSDataWavelength(dWavelength))
xsDataMOSFLMInputIndexing.setDistance(XSDataLength(dDistance))
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataImageFirst = xsDataSubWedgeFirst.getImage()[0]
strPath = xsDataImageFirst.getPath().getValue()
strFileName = os.path.basename(strPath)
strDirectory = os.path.dirname(strPath)
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFileName, "#")
xsDataMOSFLMInputIndexing.setTemplate(XSDataString(strMOSFLMTemplate))
xsDataMOSFLMInputIndexing.setDirectory(XSDataString(strDirectory))
if (xsDataCrystal is not None):
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if (xsDataSpaceGroup is not None):
xsDataStringName = xsDataSpaceGroup.getName()
if (xsDataStringName is not None):
xsDataMOSFLMInputIndexing.setSymmetry(XSDataString(xsDataStringName.getValue()))
# Loop through the list of sub wedges
for xsDataSubWedge in xsDataSubWedgeList:
xsDataImageList = xsDataSubWedge.getImage()
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition().getGoniostat()
fGonioStatOscillationStart = xsDataGoniostat.getRotationAxisStart().getValue()
fGonioStatOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
# First find the lowest image number
iLowestImageNumber = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iLowestImageNumber is None):
iLowestImageNumber = iImageNumber
elif (iImageNumber < iLowestImageNumber):
iLowestImageNumber = iImageNumber
# Loop through the list of images
for xsDataImage in xsDataImageList:
# Create the MOSFLM image object
xsDataMOSFLMImage = XSDataMOSFLMImage()
iImageNumber = xsDataImage.getNumber().getValue()
xsDataMOSFLMImage.setNumber(XSDataInteger(iImageNumber))
fImageOscillationStart = fGonioStatOscillationStart + (iImageNumber - iLowestImageNumber) * fGonioStatOscillationRange
xsDataMOSFLMImage.setRotationAxisStart(XSDataAngle(fImageOscillationStart))
xsDataMOSFLMImage.setRotationAxisEnd(XSDataAngle(fImageOscillationStart + fGonioStatOscillationRange))
xsDataMOSFLMInputIndexing.addImage(xsDataMOSFLMImage)
return xsDataMOSFLMInputIndexing
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
strAbsolutePath = os.path.abspath(strPath)
dictHeader = self.readHeaderADSC(strPath)
if (dictHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : error when reading header from %s" % strAbsolutePath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(float(dictHeader[ "BEAM_CENTER_X" ])))
xsDataDetector.setBeamPositionY(XSDataLength(float(dictHeader[ "BEAM_CENTER_Y" ])))
xsDataDetector.setDistance(XSDataLength(float(dictHeader[ "DISTANCE" ])))
fPixelSize = float(dictHeader[ "PIXEL_SIZE" ])
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSize))
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSize))
if "TWOTHETA" in dictHeader.keys():
xsDataDetector.setTwoTheta(XSDataAngle(float(dictHeader[ "TWOTHETA" ])))
xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictHeader[ "HEADER_BYTES" ])))
xsDataDetector.setSerialNumber(XSDataString(dictHeader[ "DETECTOR_SN" ]))
xsDataDetector.setNumberPixelX(XSDataInteger(int(dictHeader[ "SIZE1" ])))
xsDataDetector.setNumberPixelY(XSDataInteger(int(dictHeader[ "SIZE2" ])))
xsDataDetector.setBin(XSDataString(dictHeader[ "BIN" ]))
xsDataDetector.setDataType(XSDataString(dictHeader[ "TYPE" ]))
xsDataDetector.setByteOrder(XSDataString(dictHeader[ "BYTE_ORDER" ]))
if "CCD_IMAGE_SATURATION" in dictHeader.keys():
xsDataDetector.setImageSaturation(XSDataInteger(int(dictHeader[ "CCD_IMAGE_SATURATION" ])))
# Determine type of detector...
iNoPixelsX = xsDataDetector.getNumberPixelX().getValue()
iNoPixelsY = xsDataDetector.getNumberPixelY().getValue()
if (iNoPixelsX == 2304 and iNoPixelsY == 2304):
xsDataDetector.setName(XSDataString("ADSC Q4"))
xsDataDetector.setType(XSDataString("q4"))
elif (iNoPixelsX == 1152 and iNoPixelsY == 1152):
xsDataDetector.setName(XSDataString("ADSC Q4 bin 2x2"))
xsDataDetector.setType(XSDataString("q4-2x"))
elif (iNoPixelsX == 4096 and iNoPixelsY == 4096):
xsDataDetector.setName(XSDataString("ADSC Q210"))
xsDataDetector.setType(XSDataString("q210"))
elif (iNoPixelsX == 2048 and iNoPixelsY == 2048):
xsDataDetector.setName(XSDataString("ADSC Q210 bin 2x2"))
xsDataDetector.setType(XSDataString("q210-2x"))
elif (iNoPixelsX == 6144 and iNoPixelsY == 6144):
xsDataDetector.setName(XSDataString("ADSC Q315"))
xsDataDetector.setType(XSDataString("q315"))
elif (iNoPixelsX == 3072 and iNoPixelsY == 3072):
xsDataDetector.setName(XSDataString("ADSC Q315 bin 2x2"))
xsDataDetector.setType(XSDataString("q315-2x"))
else:
strErrorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginExecReadImageHeaderADSCv10.process", "Unknown detector type")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictHeader[ "WAVELENGTH" ])))
xsDataBeam.setExposureTime(XSDataTime(float(dictHeader[ "TIME" ])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictHeader[ "OSC_START" ])
fOscillationWidth = float(dictHeader[ "OSC_RANGE" ])
xsDataGoniostat.setRotationAxisStart(XSDataAngle(fRotationAxisStart))
xsDataGoniostat.setRotationAxisEnd(XSDataAngle(fRotationAxisStart + fOscillationWidth))
xsDataGoniostat.setOscillationWidth(XSDataAngle(fOscillationWidth))
strRotationAxis = None
if ("AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "AXIS" ]
elif ("OSC_AXIS" in dictHeader.keys()):
strRotationAxis = dictHeader[ "OSC_AXIS" ]
else:
strErrorMessage = "EDPluginExecReadImageHeaderADSCv10.process : Neither AXIS nor OSC_AXIS header item found."
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataGoniostat.setRotationAxis(XSDataString(strRotationAxis))
xsDataExperimentalCondition.setGoniostat(xsDataGoniostat)
# Create the image object
xsDataImage = XSDataImage()
xsDataImage.setPath(XSDataString(strAbsolutePath))
xsDataImage.setDate(XSDataString(dictHeader[ "DATE" ]))
strFileName = os.path.basename(strPath)
iImageNumber = EDUtilsImage.getImageNumber(strFileName)
xsDataImage.setNumber(XSDataInteger(iImageNumber))
xsDataSubWedge = XSDataSubWedge()
xsDataSubWedge.setExperimentalCondition(xsDataExperimentalCondition)
xsDataSubWedge.addImage(xsDataImage)
self.__xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.__xsDataResultReadImageHeader.setSubWedge(xsDataSubWedge)
def 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
def generateXSDataMOSFLMInputIntegration(_xsDataIntegrationInput):
"""
Translation from XSDataIntegrationInput to XSDataMOSFLMInputIntegration.
"""
EDVerbose.DEBUG(
"EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration")
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMBeamPosition
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
from XSDataMOSFLMv10 import XSDataMOSFLMNewmat
from XSDataMOSFLMv10 import XSDataMOSFLMMissettingsAngles
xsDataCrystalRefined = _xsDataIntegrationInput.getCrystalRefined()
xsDataIndexingSolutionSelected = _xsDataIntegrationInput.getSelectedIndexingSolution(
)
if (xsDataCrystalRefined is None):
xsDataCrystalRefined = xsDataIndexingSolutionSelected.getCrystal()
xsDataCollection = _xsDataIntegrationInput.getDataCollection()
xsDataSubWedge = xsDataCollection.getSubWedge()[0]
xsDataImageList = xsDataSubWedge.getImage()
xsDataImageFirst = xsDataImageList[0]
xsDataGoniostat = xsDataSubWedge.getExperimentalCondition(
).getGoniostat()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataExperimentalCondition = xsDataIndexingSolutionSelected.getExperimentalConditionRefined(
)
xsDataDetector = xsDataExperimentalCondition.getDetector()
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataMatrixA = xsDataOrientation.getMatrixA()
xsDataMatrixU = xsDataOrientation.getMatrixU()
xsDataCell = xsDataCrystal.getCell()
xsDataMOSFLMInputIntegration = XSDataMOSFLMInputIntegration()
xsDataMOSFLMNewmat = XSDataMOSFLMNewmat()
xsDataMOSFLMNewmat.setRefinedCell(xsDataCell)
xsDataMOSFLMNewmat.setAMatrix(xsDataMatrixA)
xsDataMOSFLMNewmat.setUMatrix(xsDataMatrixU)
xsDataMOSFLMInputIntegration.setMatrix(xsDataMOSFLMNewmat)
xsDataMOSFLMMissettingsAngles = XSDataMOSFLMMissettingsAngles()
xsDataMOSFLMMissettingsAngles.setPhix(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiy(XSDataAngle(0.0))
xsDataMOSFLMMissettingsAngles.setPhiz(XSDataAngle(0.0))
xsDataMOSFLMNewmat.setMissettingAngles(xsDataMOSFLMMissettingsAngles)
xsDataMOSFLMBeamPosition = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeamPosition.setX(xsDataDetector.getBeamPositionX())
xsDataMOSFLMBeamPosition.setY(xsDataDetector.getBeamPositionY())
xsDataMOSFLMInputIntegration.setBeam(xsDataMOSFLMBeamPosition)
xsDataMOSFLMInputIntegration.setMosaicity(xsDataCrystal.getMosaicity())
xsDataMOSFLMInputIntegration.setSymmetry(
xsDataCrystal.getSpaceGroup().getName())
strPathFirst = xsDataImageFirst.getPath().getValue()
strDirectoryFirst = os.path.dirname(strPathFirst)
strFilenameFirst = os.path.basename(strPathFirst)
fOscillationRange = xsDataGoniostat.getOscillationWidth().getValue()
xsDataMOSFLMInputIntegration.setWavelength(xsDataBeam.getWavelength())
xsDataMOSFLMInputIntegration.setDistance(xsDataDetector.getDistance())
xsDataMOSFLMInputIntegration.setDirectory(
XSDataString(strDirectoryFirst))
xsDataMOSFLMInputIntegration.setOscillationWidth(
XSDataAngle(fOscillationRange))
xsDataMOSFLMDetector = EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector(
xsDataDetector)
xsDataMOSFLMInputIntegration.setDetector(xsDataMOSFLMDetector)
strMOSFLMTemplate = EDUtilsImage.getTemplate(strFilenameFirst, "#")
xsDataMOSFLMInputIntegration.setTemplate(
XSDataString(strMOSFLMTemplate))
iImageStart = None
iImageEnd = None
for xsDataImage in xsDataImageList:
iImageNumber = xsDataImage.getNumber().getValue()
if (iImageStart is None):
iImageStart = iImageNumber
elif (iImageStart > iImageNumber):
iImageStart = iImageNumber
if (iImageEnd is None):
iImageEnd = iImageNumber
elif (iImageEnd < iImageNumber):
iImageEnd = iImageNumber
xsDataMOSFLMInputIntegration.setImageStart(XSDataInteger(iImageStart))
xsDataMOSFLMInputIntegration.setImageEnd(XSDataInteger(iImageEnd))
xsDataMOSFLMInputIntegration.setRotationAxisStart(
xsDataGoniostat.getRotationAxisStart())
# print xsDataMOSFLMInputIntegration.marshal()
return xsDataMOSFLMInputIntegration
def generateDataCollectionDescriptorForSubWedge(self, calibDate, omegaR, kappaR, phiR, beamD, polarisationP, exposuretime, imagewidth, numberimages, wavelength, OmegaV, KappaV, PhiV, imgFnames):
##CONTAINER
self.xsDC_v2 = XSDataCollection_v2()
##GonioCalib
calib = XSDataMXv2.XSCalibration()
cdate = XSDataMXv2.XSDataDate()
cdate.setValue(XSDataMXv2.XSDataString(calibDate))
calib.setDate(cdate)
#OmegaCalib
omegacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(omegaR[0])
zdir.setV2(omegaR[1])
zdir.setV3(omegaR[2])
omegacal.setZerodirection(zdir)
omegacal.setXSCalibration(calib)
#KappaCalib
kappacal = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(kappaR[0])
zdir.setV2(kappaR[1])
zdir.setV3(kappaR[2])
kappacal.setZerodirection(zdir)
kappacal.setXSCalibration(calib)
#PhiCalib
phical = XSDataMXv2.XSCalibratedDisplacementAxis()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(phiR[0])
zdir.setV2(phiR[1])
zdir.setV3(phiR[2])
phical.setZerodirection(zdir)
phical.setXSCalibration(calib)
##goni
actgonio = XSDataMXv2.XSRotationalGoniostat()
#omega
omega = XSDataMXv2.XSGoniostatBaseAxis()
omega.setName(XSDataMXv2.XSDataString('Omega'))
omega.setIsscannable(XSDataMXv2.XSDataBoolean(1))
omega.addXSCalibratedDisplacementAxis(omegacal)
actgonio.setXSGoniostatBaseAxis(omega)
#kappa
kappa = XSDataMXv2.XSGoniostatRotatableAxis()
kappa.setName(XSDataMXv2.XSDataString('Kappa'))
kappa.setIsscannable(XSDataMXv2.XSDataBoolean(0))
kappa.addXSCalibratedDisplacementAxis(kappacal)
actgonio.addXSGoniostatRotatableAxis(kappa)
#phi
phi = XSDataMXv2.XSGoniostatRotatableAxis()
phi.setName(XSDataMXv2.XSDataString('Phi'))
phi.setIsscannable(XSDataMXv2.XSDataBoolean(0))
phi.addXSCalibratedDisplacementAxis(phical)
actgonio.addXSGoniostatRotatableAxis(phi)
##beam
beam = XSDataMXv2.XSBeam()
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(polarisationP[0])
zdir.setV2(polarisationP[1])
zdir.setV3(polarisationP[2])
beam.setPolarisatation(zdir)
zdir = XSDataMXv2.XSDataUnitVector()
zdir.setV1(beamD[0])
zdir.setV2(beamD[1])
zdir.setV3(beamD[2])
beam.setDirection(zdir)
##detector
detector = XSDataMXv2.XSDetector()
detector.setName(XSDataMXv2.XSDataString('detector'))
###detector.set
##SUBWEDGE
sw = XSSubWedge_v2()
# template
sw.setImagefilenametemplate(XSDataMXv2.XSDataString(EDUtilsImage.getTemplate(imgFnames[0], "#")))
# images
for imgFname in imgFnames:
img = XSDiffractionImages_v2()
img.setFilename(XSDataMXv2.XSDataString(imgFname))
sw.addXSDiffractionImages(img)
#RotationExposure
rotexp = XSRotationExposure_v2()
rotexp.setExposuretime(XSDataMXv2.XSDataTime(exposuretime))
rotexp.setImagewidth(XSDataMXv2.XSDataAngle(imagewidth))
rotexp.setNumberimages(XSDataMXv2.XSDataInteger(numberimages))
rotexp.setXSGoniostatAxis(omega)
sw.setXSRotationExposure(rotexp)
#Beamsetting
beams = XSBeamSetting_v2()
w = XSDataMXv2.XSDataWavelength()
w.setValue(wavelength)
beams.setWavelength(w)
beams.setXSBeam(beam)
sw.setXSBeamSetting(beams)
#RotationalGonioSetting
rotgset = XSDataMXv2.XSRotationalGoniostatSetting()
rotgset.setXSRotationalGoniostat(actgonio)
oang = XSDataMXv2.XSDataAngle()
oang.setValue(OmegaV)
rotgset.setBaseaxissetting(oang)
kang = XSDataMXv2.XSDataAngle()
kang.setValue(KappaV)
rotgset.addAxissetting(kang)
pang = XSDataMXv2.XSDataAngle()
pang.setValue(PhiV)
rotgset.addAxissetting(pang)
sw.setXSRotationalGoniostatSetting(rotgset)
#DetectorSetting TODOTODO
detset = XSDataMXv2.XSDetectorSetting()
#axissetting=(XSDataMXv2.XSDataAngle().setValue(KappaV),XSDataMXv2.XSDataAngle().setValue(PhiV))
#detset.setAxissetting(axissetting)
self.xsDC_v2.addXSSubWedge(sw)
imgFname = self.xsDataResultSubWedgeAssemble.getSubWedge()[0].getImage()[0].getPath().getValue()
self.xsDC_v2.outputFile(os.path.dirname(imgFname) + '/edna_' + EDUtilsImage.getTemplate(imgFname, "#") + '_auto')
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.process")
xsDataInputReadImageHeader = self.getDataInput()
xsDataFile = xsDataInputReadImageHeader.getImage()
strPath = xsDataFile.getPath().getValue()
dictPilatus2MHeader = self.readHeaderPilatus2M(strPath)
if (dictPilatus2MHeader is None):
strErrorMessage = "EDPluginExecReadImageHeaderPilatus2Mv10.process : Cannot read header : %s" % strPath
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
xsDataExperimentalCondition = XSDataExperimentalCondition()
xsDataDetector = XSDataDetector()
iNoPixelsX = 1475
iNoPixelsY = 1679
xsDataDetector.setNumberPixelX(XSDataInteger(iNoPixelsX))
xsDataDetector.setNumberPixelY(XSDataInteger(iNoPixelsY))
# Pixel size
listPixelSizeXY = dictPilatus2MHeader[ "Pixel_size" ].split(" ")
fPixelSizeX = float(listPixelSizeXY[0]) * 1000
xsDataDetector.setPixelSizeX(XSDataLength(fPixelSizeX))
fPixelSizeY = float(listPixelSizeXY[3]) * 1000
xsDataDetector.setPixelSizeY(XSDataLength(fPixelSizeY))
# Beam position
listBeamPosition = dictPilatus2MHeader["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(dictPilatus2MHeader[ "Detector_distance" ].split(" ")[0]) * 1000
xsDataDetector.setDistance(XSDataLength(fDistance))
# xsDataDetector.setNumberBytesInHeader(XSDataInteger(float(dictPilatus2MHeader[ "header_size" ])))
xsDataDetector.setSerialNumber(XSDataString(dictPilatus2MHeader[ "Detector:" ]))
# #xsDataDetector.setBin( XSDataString( dictPilatus2MHeader[ "BIN" ] ) ) )
# #xsDataDetector.setDataType( XSDataString( dictPilatus2MHeader[ "TYPE" ] ) ) )
# #xsDataDetector.setByteOrder( XSDataString( dictPilatus2MHeader[ "BYTE_ORDER" ] ) ) )
# xsDataDetector.setImageSaturation(XSDataInteger(int(dictPilatus2MHeader[ "saturation_level" ])))
xsDataDetector.setName(XSDataString("PILATUS2 3M"))
xsDataDetector.setType(XSDataString("pilatus2m"))
xsDataExperimentalCondition.setDetector(xsDataDetector)
# Beam object
xsDataBeam = XSDataBeam()
xsDataBeam.setWavelength(XSDataWavelength(float(dictPilatus2MHeader[ "Wavelength" ].split(" ")[0])))
xsDataBeam.setExposureTime(XSDataTime(float(dictPilatus2MHeader[ "Exposure_time" ].split(" ")[0])))
xsDataExperimentalCondition.setBeam(xsDataBeam)
# Goniostat object
xsDataGoniostat = XSDataGoniostat()
fRotationAxisStart = float(dictPilatus2MHeader[ "Start_angle" ].split(" ")[0])
fOscillationWidth = float(dictPilatus2MHeader[ "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 dictPilatus2MHeader:
strTimeStamp = dictPilatus2MHeader[ "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 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 generateCommands(self, _xsDataInputH5ToCBF):
"""
This method creates a list of commands for the converter
"""
self.DEBUG("EDPluginH5ToCBFv1_1.generateCommands")
hdf5File = _xsDataInputH5ToCBF.hdf5File.path.value
directory = os.path.dirname(hdf5File)
prefix = EDUtilsImage.getPrefix(hdf5File)
if _xsDataInputH5ToCBF.imageNumber is not None:
imageNumber = _xsDataInputH5ToCBF.imageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
if EDUtilsPath.isEMBL():
masterFile = os.path.join(directory, prefix + "_master.h5".format(hdf5ImageNumber))
else:
masterFile = os.path.join(directory, prefix + "_{0}_master.h5".format(hdf5ImageNumber))
if _xsDataInputH5ToCBF.forcedOutputImageNumber is not None:
CBFFileName = prefix + "_%04d" % _xsDataInputH5ToCBF.forcedOutputImageNumber.value + ".cbf"
imageNumberInHdf5File = imageNumber
else:
CBFFileName = prefix + "_%04d" % imageNumber + ".cbf"
imageNumberInHdf5File = imageNumber - hdf5ImageNumber + 1
tmpCBFFileName = "tmp_" + CBFFileName
if _xsDataInputH5ToCBF.forcedOutputDirectory is None:
self.CBFFile = os.path.join(directory, CBFFileName)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0o755)
self.CBFFile = os.path.join(forcedOutputDirectory, CBFFileName)
scriptCommandLine = "{0} {1} {2}".format(masterFile, imageNumberInHdf5File, self.CBFFile)
elif _xsDataInputH5ToCBF.startImageNumber is not None and _xsDataInputH5ToCBF.endImageNumber is not None:
startImageNumber = _xsDataInputH5ToCBF.startImageNumber.value
endImageNumber = _xsDataInputH5ToCBF.endImageNumber.value
if _xsDataInputH5ToCBF.hdf5ImageNumber is None:
hdf5ImageNumber = startImageNumber
else:
hdf5ImageNumber = _xsDataInputH5ToCBF.hdf5ImageNumber.value
if "master" in hdf5File:
masterFile = hdf5File
else:
masterFile = os.path.join(directory, prefix + "_{0}_master.h5".format(hdf5ImageNumber))
CBFFileNamePrefix = prefix + "_"
if _xsDataInputH5ToCBF.forcedOutputDirectory is None:
CBFFilePath = os.path.join(directory, CBFFileNamePrefix)
else:
forcedOutputDirectory = self.dataInput.forcedOutputDirectory.path.value
if not os.path.exists(forcedOutputDirectory):
os.makedirs(forcedOutputDirectory, 0o755)
CBFFilePath = os.path.join(forcedOutputDirectory, CBFFileNamePrefix)
scriptCommandLine = "{0} {1}:{2} {3}".format(masterFile, startImageNumber, endImageNumber, CBFFilePath)
self.CBFFileTemplate = CBFFilePath + "######.cbf"
return scriptCommandLine
def process(self, _edPlugin=None):
"""
Executes the execution plugins
"""
EDPluginControl.process(self, _edPlugin)
self.DEBUG("EDPluginControlImageQualityIndicatorsv1_4.process")
EDUtilsParallel.initializeNbThread()
# Check batch size
if self.dataInput.batchSize is None:
batchSize = 1
else:
batchSize = self.dataInput.batchSize.value
self.screen("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
# Loop through all the incoming reference images
listXSDataImage = self.dataInput.image
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
self.xsDataResultControlImageQualityIndicators = XSDataResultControlImageQualityIndicators()
listPluginDistl = []
listPluginDozor = []
listBatch = []
indexBatch = 0
listH5FilePath = []
ispybDataCollection = None
for xsDataImage in listXSDataImage:
strPathToImage = xsDataImage.path.value
# If Eiger, just wait for the h5 file
if "id30a3" in strPathToImage:
h5MasterFilePath, h5DataFilePath, hdf5ImageNumber = self.getH5FilePath(strPathToImage, batchSize)
# 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")
ispybDataCollection = None
time.sleep(1)
indexLoop = 1
continueLoop = True
while continueLoop:
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(strPathToImage))
imageNumber = EDUtilsImage.getImageNumber(strPathToImage)
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(imageNumber)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputControlH5ToCBF.ispybDataCollection = ispybDataCollection
edPluginControlH5ToCBF = self.loadPlugin(self.strPluginControlH5ToCBF, "ControlH5ToCBF_%04d_%02d" % (imageNumber, indexLoop))
edPluginControlH5ToCBF.dataInput = xsDataInputControlH5ToCBF
edPluginControlH5ToCBF.executeSynchronous()
cbfFile = edPluginControlH5ToCBF.dataOutput.outputCBFFile
# print(cbfFile)
# print(indexLoop)
if cbfFile is not None:
strPathToImage = cbfFile.path.value
# print(cbfFile.path.value)
if os.path.exists(strPathToImage):
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
ispybDataCollection = edPluginControlH5ToCBF.dataOutput.ispybDataCollection
elif 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.DEBUG("Wait file timeOut set to %f" % 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()
else:
# Check if we should run distl.signalStrength
xsDataImageNew = XSDataImage(XSDataString(strPathToImage))
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))
listBatch.append(xsDataImageNew.copy())
if len(listBatch) == batchSize:
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append((edPluginControlDozor, listBatch))
listBatch = []
if len(listBatch) > 0:
# Process the remaining images...
edPluginControlDozor = self.loadPlugin(self.strPluginNameControlDozor)
xsDataInputControlDozor = XSDataInputControlDozor()
for image in listBatch:
xsDataInputControlDozor.addImage(XSDataFile(image.path))
xsDataInputControlDozor.batchSize = XSDataInteger(batchSize)
edPluginControlDozor.dataInput = xsDataInputControlDozor
edPluginControlDozor.execute()
listPluginDozor.append([edPluginControlDozor, listBatch])
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.imageQualityIndicators is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators.parseString(\
edPluginPluginExecImageQualityIndicator.dataOutput.imageQualityIndicators.marshal())
self.xsDataResultControlImageQualityIndicators.addImageQualityIndicators(xsDataImageQualityIndicators)
for (edPluginControlDozor, listBatch) in listPluginDozor:
edPluginControlDozor.synchronize()
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
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.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