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 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 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 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 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 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 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 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 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 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):
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 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 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 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 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 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):
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)
if sys.argv[index] == "--image":
index += 1
while not sys.argv[index].startswith("--"):
listImages.append(sys.argv[index])
# Replace the .h5 image file suffix with .cbf
sys.argv[index] = os.path.splitext(sys.argv[index])[0] + ".cbf"
index += 1
break
if len(listImages) == 0:
print("No --image keyword found!")
sys.exit(1)
# Find the series number
firstImagePath = listImages[0]
imagePrefixAndRunNumber = EDUtilsImage.getPrefix(firstImagePath)
imageDirectory = os.path.dirname(firstImagePath)
if imageDirectory == "":
imageDirectory = os.getcwd()
listFilePath = glob.glob(
os.path.join(imageDirectory, imagePrefixAndRunNumber + "*"))
listH5Number = []
listSerialNumber = []
#
# NSLS Eiger HDF 5 naming convention, e.g.:
# ref-XtalSamp_3_4_10_master.h5 ref-XtalSamp_3_4_11_master.h5
# ref-XtalSamp_3_4_10_data_000001.h5 ref-XtalSamp_3_4_11_data_000001.h5
#
p = re.compile('{0}_(?P<serialNumber>\d+)_data_(?P<imageNumber>\d+).h5'.format(
imagePrefixAndRunNumber))
firstSerialNumber = None
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 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 testGetPrefix(self):
strPrefix = EDUtilsImage.getPrefix(self.__strFileName)
EDAssert.equal("ref-testscale_1", strPrefix)
def testGetHDF5Prefix(self):
strHDF5FileName = "t20keV-insulin_4_1_master.h5"
strPrefix = EDUtilsImage.getPrefix(strHDF5FileName)
EDAssert.equal("t20keV-insulin_4", strPrefix)
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
if sys.argv[index] == "--image":
index += 1
while not sys.argv[index].startswith("--"):
listImages.append(sys.argv[index])
# Replace the .h5 image file suffix with .cbf
sys.argv[index] = os.path.splitext(sys.argv[index])[0] + ".cbf"
index += 1
break
if len(listImages) == 0:
print("No --image keyword found!")
sys.exit(1)
# Find the series number
firstImagePath = listImages[0]
imagePrefixAndRunNumber = EDUtilsImage.getPrefix(firstImagePath)
imageDirectory = os.path.dirname(firstImagePath)
if imageDirectory == "":
imageDirectory = os.getcwd()
listFilePath = glob.glob(os.path.join(imageDirectory, imagePrefixAndRunNumber + "*"))
listH5Number = []
listSerialNumber = []
#
# NSLS Eiger HDF 5 naming convention, e.g.:
# ref-XtalSamp_3_4_10_master.h5 ref-XtalSamp_3_4_11_master.h5
# ref-XtalSamp_3_4_10_data_000001.h5 ref-XtalSamp_3_4_11_data_000001.h5
#
p = re.compile('{0}_(?P<serialNumber>\d+)_data_(?P<imageNumber>\d+).h5'.format(imagePrefixAndRunNumber))
firstSerialNumber = None
for filePath in listFilePath:
# Regular expression, looking for <prefix>_<runnumber>_data_<serialNumber>.h5
