def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.DEBUG("EDPluginControlReadImageHeaderv10.finallyProcess")
if self.xsDataResultReadImageHeader is None:
# Create empty xsDataResult
self.xsDataResultReadImageHeader = XSDataResultReadImageHeader()
self.setDataOutput(self.xsDataResultReadImageHeader)
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)
class EDPluginExecReadImageHeaderPilatus2Mv10(EDPluginExec):
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputReadImageHeader)
self.__xsDataResultReadImageHeader = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
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 postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.postProcess")
if (self.__xsDataResultReadImageHeader is not None):
self.setDataOutput(self.__xsDataResultReadImageHeader)
def readHeaderPilatus2M(self, _strImageFileName):
"""
Returns an dictionary with the contents of a Pilatus 6M CBF image header.
"""
dictPilatus2M = None
pyFile = None
try:
pyFile = open(_strImageFileName, "r")
except:
EDVerbose.ERROR("EDPluginExecReadImageHeaderPilatus2Mv10.readHeaderPilauts6M: couldn't open file: " + _strImageFileName)
self.setFailure()
if (pyFile != None):
EDVerbose.DEBUG("EDPluginExecReadImageHeaderPilatus2Mv10.readHeaderPilauts6M: Reading header from image " + _strImageFileName)
pyFile.seek(0, 0)
bContinue = True
iMax = 60
iIndex = 0
while bContinue:
strLine = pyFile.readline()
iIndex += 1
if (strLine.find("_array_data.header_contents") != -1):
dictPilatus2M = {}
if (strLine.find("_array_data.data") != -1) or iIndex > iMax:
bContinue = False
if (dictPilatus2M != None) and (strLine[0] == "#"):
# Check for date
strTmp = strLine[2:].replace("\r\n", "")
if strLine[6] == "/" and strLine[10] == "/":
dictPilatus2M["DateTime"] = strTmp
else:
strKey = strTmp.split(" ")[0]
strValue = strTmp.replace(strKey, "")[1:]
dictPilatus2M[strKey] = strValue
pyFile.close()
return dictPilatus2M
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)
class EDPluginExecReadImageHeaderEiger4Mv10(EDPluginExec):
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputReadImageHeader)
self.__xsDataResultReadImageHeader = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
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 postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.postProcess")
if (self.__xsDataResultReadImageHeader is not None):
self.setDataOutput(self.__xsDataResultReadImageHeader)
def readHeaderEiger4M(self, _strImageFileName):
"""
Returns an dictionary with the contents of a Pilatus 6M CBF image header.
"""
dictEiger4M = None
pyFile = None
try:
pyFile = open(_strImageFileName, "rb")
except:
self.ERROR("EDPluginExecReadImageHeaderEiger4Mv10.readHeaderEiger4M: couldn't open file: " + _strImageFileName)
self.setFailure()
if (pyFile != None):
self.DEBUG("EDPluginExecReadImageHeaderEiger4Mv10.readHeaderEiger4M: Reading header from image " + _strImageFileName)
pyFile.seek(0, 0)
bContinue = True
iMax = 60
iIndex = 0
while bContinue:
strLine = pyFile.readline().decode('utf-8')
iIndex += 1
if (strLine.find("_array_data.header_contents") != -1):
dictEiger4M = {}
if (strLine.find("_array_data.data") != -1) or iIndex > iMax:
bContinue = False
if (dictEiger4M != None) and (strLine[0] == "#"):
# Check for date
strTmp = strLine[2:].replace("\r\n", "")
if strLine[6] == "/" and strLine[10] == "/":
dictEiger4M["DateTime"] = strTmp
else:
strKey = strTmp.split(" ")[0]
strValue = strTmp.replace(strKey, "")[1:]
dictEiger4M[strKey] = strValue
pyFile.close()
return dictEiger4M
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)
class EDPluginExecReadImageHeaderADSCv10(EDPluginExec):
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputReadImageHeader)
self.__xsDataResultReadImageHeader = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
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 postProcess(self, _edObject=None):
EDPlugin.postProcess(self)
EDVerbose.DEBUG("*** EDPluginExecReadImageHeaderADSCv10.postProcess")
if (self.__xsDataResultReadImageHeader is not None):
self.setDataOutput(self.__xsDataResultReadImageHeader)
def readHeaderADSC(self, _strImageFileName):
"""
This method reads the header from an ADSC image and returns a dictionary.
Ideally this method should be a part of another (exec) plugin.
"""
pyFile = None
dictionary = None
try:
pyFile = open(_strImageFileName, "r")
except:
EDVerbose.warning("**** EDPluginExecReadImageHeaderADSCv10.readHeaderADSC: couldn't open file: " + _strImageFileName)
if (pyFile != None):
EDVerbose.DEBUG("EDPluginExecReadImageHeaderADSCv10.readHeaderADSC: Reading header from image " + _strImageFileName)
pyFile.seek(0, 0)
strLine = pyFile.readline()
if strLine[0] == "{":
dictionary = {}
strLine = pyFile.readline()
while strLine[0] != "}" :
listSplit = strLine.split("=")
strKeyword = listSplit[0]
listSplitValue = listSplit[1].split(";")
strValue = listSplitValue[0]
dictionary[strKeyword] = strValue
strLine = pyFile.readline()
pyFile.close()
return dictionary
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)
class EDPluginExecReadImageHeaderMARCCDv10(EDPluginExec):
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputReadImageHeader)
self.__xsDataResultReadImageHeader = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
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 postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.postProcess")
if (self.__xsDataResultReadImageHeader is not None):
self.setDataOutput(self.__xsDataResultReadImageHeader)
def readHeaderMarccd(self, _strFileName):
"""
Returns an dictionary with the contents of a MAR CCD image header.
"""
#
# Created by Krister Larsson on 08/11/5.
# Modified by Olof Svensson 20090401
#
strUint32 = 'I'
strChar = 's'
# strInt16 = 'H'
strInt32 = 'i'
iMAXIMAGES = 9
pyListHeader = [
# File/header format parameters (256bytes)
[strUint32, 'header_type'],
[strChar, 'header_name', 16],
[strUint32, 'header_major_version'],
[strUint32, 'header_minor_version'],
[strUint32, 'header_byte_order'],
[strUint32, 'data_byte_order'],
[strUint32, 'header_size'],
[strUint32, 'frame_type'],
[strUint32, 'magic_number'],
[strUint32, 'compression_type'],
[strUint32, 'compression1'],
[strUint32, 'compression2'],
[strUint32, 'compression3'],
[strUint32, 'compression4'],
[strUint32, 'compression5'],
[strUint32, 'compression6'],
[strUint32, 'nheaders'],
[strUint32, 'nfast'],
[strUint32, 'nslow'],
[strUint32, 'depth'],
[strUint32, 'record_length'],
[strUint32, 'signif_bits'],
[strUint32, 'data_type'],
[strUint32, 'saturated_value'],
[strUint32, 'sequence'],
[strUint32, 'nimages'],
[strUint32, 'origin'],
[strUint32, 'orientation'],
[strUint32, 'view_direction'],
[strUint32, 'overflow_direction'],
[strUint32, 'over_8_bits'],
[strUint32, 'over_16_bits'],
[strUint32, 'multiplexed'],
[strUint32, 'nfastimages'],
[strUint32, 'nslowimages'],
[strUint32, 'darkcurrent_applied'],
[strUint32, 'bias_applied'],
[strUint32, 'flatfield_applied'],
[strUint32, 'distortion_applied'],
[strUint32, 'original_header_type'],
[strUint32, 'file_saved'],
[strUint32, 'n_valid_pixels'],
[strUint32, 'defectmap_applied'],
[strUint32, 'subimage_nfast'],
[strUint32, 'subimage_nslow'],
[strUint32, 'subimage_origin_fast'],
[strUint32, 'subimage_origin_slow'],
[strUint32, 'readout_pattern'],
[strUint32, 'saturation_level'],
[strUint32, 'orientation_code'],
[strUint32, 'frameshift_multiplexed'],
[strUint32, 'precsan_nfast'],
[strUint32, 'prescan_nslow'],
[strUint32, 'postscan_nfast'],
[strUint32, 'postscan_nslow'],
[strUint32, 'prepost_trimmed'],
[strChar, 'reserve1', 20],
# Data statistics (128 bytes)
[strUint32, 'total_counts', 2],
[strUint32, 'special_counts1', 2],
[strUint32, 'special_counts2', 2],
[strUint32, 'min'],
[strUint32, 'max'],
[strUint32, 'mean'],
[strUint32, 'rms'],
[strUint32, 'n_zeros'],
[strUint32, 'n_saturated'],
[strUint32, 'stats_uptodate'],
[strUint32, 'pixel_noise', iMAXIMAGES],
[strChar, 'reserve2', (19 - iMAXIMAGES) * 4 ],
# More statistics (256 bytes)
# [uint16,'percentile',128],
# Percentile is substituted by Sample changer info
[strChar, 'barcode', 16],
[strUint32, 'barcode_angle'],
[strUint32, 'barcode_status'],
[strChar, 'reserve2a', 232],
# Goniostat parameters (128 bytes)
[strInt32, 'xtal_to_detector'],
[strInt32, 'beam_x'],
[strInt32, 'beam_y'],
[strInt32, 'integration_time'],
[strInt32, 'exposure_time'],
[strInt32, 'readout_time'],
[strInt32, 'nreads'],
[strInt32, 'start_twotheta'],
[strInt32, 'start_omega'],
[strInt32, 'start_chi'],
[strInt32, 'start_kappa'],
[strInt32, 'start_phi'],
[strInt32, 'start_delta'],
[strInt32, 'start_gamma'],
[strInt32, 'start_xtal_to_detector'],
[strInt32, 'end_twotheta'],
[strInt32, 'end_omega'],
[strInt32, 'end_chi'],
[strInt32, 'end_kappa'],
[strInt32, 'end_phi'],
[strInt32, 'end_delta'],
[strInt32, 'end_gamma'],
[strInt32, 'end_xtal_to_detector'],
[strInt32, 'rotation_axis'],
[strInt32, 'rotation_range'],
[strInt32, 'detector_rotx'],
[strInt32, 'detector_roty'],
[strInt32, 'detector_rotz'],
[strInt32, 'total_dose'],
[strChar, 'reserve3', 12],
# Detector parameters (128 bytes)
[strInt32, 'detector_type'],
[strInt32, 'pixelsize_x'],
[strInt32, 'pixelsize_y'],
[strInt32, 'mean_bias'],
[strInt32, 'photons_per_100adu'],
[strInt32, 'measured_bias', iMAXIMAGES],
[strInt32, 'measured_temperature', iMAXIMAGES],
[strInt32, 'measured_pressure', iMAXIMAGES],
# X-ray source and optics parameters (128 bytes)
[strInt32, 'source_type'],
[strInt32, 'source_dx'],
[strInt32, 'source_dy'],
[strInt32, 'source_wavelength'],
[strInt32, 'source_power'],
[strInt32, 'source_voltage'],
[strInt32, 'source_current'],
[strInt32, 'source_bias'],
[strInt32, 'source_polarization_x'],
[strInt32, 'source_polarization_y'],
[strInt32, 'source_intensity_0'],
[strInt32, 'source_intensity_1'],
[strChar, 'reserve_source', 8],
[strInt32, 'optics_type'],
[strInt32, 'optics_dx'],
[strInt32, 'optics_dy'],
[strInt32, 'optics_wavelength'],
[strInt32, 'optics_dispersion'],
[strInt32, 'optics_crossfire_x'],
[strInt32, 'optics_crossfire_y'],
[strInt32, 'optics_angle'],
[strInt32, 'optics_polarization_x'],
[strInt32, 'optics_polarization_y'],
[strChar, 'reserve_optics', 16],
[strChar, 'reserve5', 16],
# File parameters
[strChar, 'filetitle', 128],
[strChar, 'filepath', 128],
[strChar, 'filename', 64],
[strChar, 'acquire_timestamp', 32],
[strChar, 'header_timestamp', 32],
[strChar, 'save_timestamp', 32],
[strChar, 'file_comment', 512],
[strChar, 'reserve6', 96],
[strChar, 'dataset_comments', 512],
[strChar, 'user_data', 512]
]
pyFile = None
dictMarccd = None
try:
pyFile = open(_strFileName, "rb")
except:
EDVerbose.warning("EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: couldn't open file: " + _strFileName)
if (pyFile is not None):
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: Reading header from image " + _strFileName)
dictMarccd = {}
# Move to marccd part of header
pyFile.seek(1024)
for pyListRow in pyListHeader:
if len(pyListRow) == 3:
strFormat = str(pyListRow[2]) + str(pyListRow[0])
else:
strFormat = pyListRow[0]
strKeyword = pyListRow[1]
iReadSize = struct.calcsize(strFormat)
pyRawData = pyFile.read(iReadSize)
strValue = struct.unpack(strFormat, pyRawData)
if len(strValue) == 1:
strValue = strValue[0]
if pyListRow[0] == strChar:
strValue = strValue.strip('\x00')
dictMarccd[strKeyword] = strValue
pyFile.close()
return dictMarccd
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)
class EDPluginExecReadImageHeaderMARCCDv10(EDPluginExec):
def __init__(self):
"""
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataInputReadImageHeader)
self.__xsDataResultReadImageHeader = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
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 postProcess(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("EDPluginExecReadImageHeaderMARCCDv10.postProcess")
if (self.__xsDataResultReadImageHeader is not None):
self.setDataOutput(self.__xsDataResultReadImageHeader)
def readHeaderMarccd(self, _strFileName):
"""
Returns an dictionary with the contents of a MAR CCD image header.
"""
#
# Created by Krister Larsson on 08/11/5.
# Modified by Olof Svensson 20090401
#
strUint32 = 'I'
strChar = 's'
#strInt16 = 'H'
strInt32 = 'i'
iMAXIMAGES = 9
pyListHeader = [
#File/header format parameters (256bytes)
[strUint32, 'header_type'],
[strChar, 'header_name', 16],
[strUint32, 'header_major_version'],
[strUint32, 'header_minor_version'],
[strUint32, 'header_byte_order'],
[strUint32, 'data_byte_order'],
[strUint32, 'header_size'],
[strUint32, 'frame_type'],
[strUint32, 'magic_number'],
[strUint32, 'compression_type'],
[strUint32, 'compression1'],
[strUint32, 'compression2'],
[strUint32, 'compression3'],
[strUint32, 'compression4'],
[strUint32, 'compression5'],
[strUint32, 'compression6'],
[strUint32, 'nheaders'],
[strUint32, 'nfast'],
[strUint32, 'nslow'],
[strUint32, 'depth'],
[strUint32, 'record_length'],
[strUint32, 'signif_bits'],
[strUint32, 'data_type'],
[strUint32, 'saturated_value'],
[strUint32, 'sequence'],
[strUint32, 'nimages'],
[strUint32, 'origin'],
[strUint32, 'orientation'],
[strUint32, 'view_direction'],
[strUint32, 'overflow_direction'],
[strUint32, 'over_8_bits'],
[strUint32, 'over_16_bits'],
[strUint32, 'multiplexed'],
[strUint32, 'nfastimages'],
[strUint32, 'nslowimages'],
[strUint32, 'darkcurrent_applied'],
[strUint32, 'bias_applied'],
[strUint32, 'flatfield_applied'],
[strUint32, 'distortion_applied'],
[strUint32, 'original_header_type'],
[strUint32, 'file_saved'],
[strUint32, 'n_valid_pixels'],
[strUint32, 'defectmap_applied'],
[strUint32, 'subimage_nfast'],
[strUint32, 'subimage_nslow'],
[strUint32, 'subimage_origin_fast'],
[strUint32, 'subimage_origin_slow'],
[strUint32, 'readout_pattern'],
[strUint32, 'saturation_level'],
[strUint32, 'orientation_code'],
[strUint32, 'frameshift_multiplexed'],
[strUint32, 'precsan_nfast'],
[strUint32, 'prescan_nslow'],
[strUint32, 'postscan_nfast'],
[strUint32, 'postscan_nslow'],
[strUint32, 'prepost_trimmed'],
[strChar, 'reserve1', 20],
#Data statistics (128 bytes)
[strUint32, 'total_counts', 2],
[strUint32, 'special_counts1', 2],
[strUint32, 'special_counts2', 2],
[strUint32, 'min'],
[strUint32, 'max'],
[strUint32, 'mean'],
[strUint32, 'rms'],
[strUint32, 'n_zeros'],
[strUint32, 'n_saturated'],
[strUint32, 'stats_uptodate'],
[strUint32, 'pixel_noise', iMAXIMAGES],
[strChar, 'reserve2', (19 - iMAXIMAGES) * 4],
#More statistics (256 bytes)
#[uint16,'percentile',128],
#Percentile is substituted by Sample changer info
[strChar, 'barcode', 16],
[strUint32, 'barcode_angle'],
[strUint32, 'barcode_status'],
[strChar, 'reserve2a', 232],
#Goniostat parameters (128 bytes)
[strInt32, 'xtal_to_detector'],
[strInt32, 'beam_x'],
[strInt32, 'beam_y'],
[strInt32, 'integration_time'],
[strInt32, 'exposure_time'],
[strInt32, 'readout_time'],
[strInt32, 'nreads'],
[strInt32, 'start_twotheta'],
[strInt32, 'start_omega'],
[strInt32, 'start_chi'],
[strInt32, 'start_kappa'],
[strInt32, 'start_phi'],
[strInt32, 'start_delta'],
[strInt32, 'start_gamma'],
[strInt32, 'start_xtal_to_detector'],
[strInt32, 'end_twotheta'],
[strInt32, 'end_omega'],
[strInt32, 'end_chi'],
[strInt32, 'end_kappa'],
[strInt32, 'end_phi'],
[strInt32, 'end_delta'],
[strInt32, 'end_gamma'],
[strInt32, 'end_xtal_to_detector'],
[strInt32, 'rotation_axis'],
[strInt32, 'rotation_range'],
[strInt32, 'detector_rotx'],
[strInt32, 'detector_roty'],
[strInt32, 'detector_rotz'],
[strInt32, 'total_dose'],
[strChar, 'reserve3', 12],
#Detector parameters (128 bytes)
[strInt32, 'detector_type'],
[strInt32, 'pixelsize_x'],
[strInt32, 'pixelsize_y'],
[strInt32, 'mean_bias'],
[strInt32, 'photons_per_100adu'],
[strInt32, 'measured_bias', iMAXIMAGES],
[strInt32, 'measured_temperature', iMAXIMAGES],
[strInt32, 'measured_pressure', iMAXIMAGES],
#X-ray source and optics parameters (128 bytes)
[strInt32, 'source_type'],
[strInt32, 'source_dx'],
[strInt32, 'source_dy'],
[strInt32, 'source_wavelength'],
[strInt32, 'source_power'],
[strInt32, 'source_voltage'],
[strInt32, 'source_current'],
[strInt32, 'source_bias'],
[strInt32, 'source_polarization_x'],
[strInt32, 'source_polarization_y'],
[strInt32, 'source_intensity_0'],
[strInt32, 'source_intensity_1'],
[strChar, 'reserve_source', 8],
[strInt32, 'optics_type'],
[strInt32, 'optics_dx'],
[strInt32, 'optics_dy'],
[strInt32, 'optics_wavelength'],
[strInt32, 'optics_dispersion'],
[strInt32, 'optics_crossfire_x'],
[strInt32, 'optics_crossfire_y'],
[strInt32, 'optics_angle'],
[strInt32, 'optics_polarization_x'],
[strInt32, 'optics_polarization_y'],
[strChar, 'reserve_optics', 16],
[strChar, 'reserve5', 16],
#File parameters
[strChar, 'filetitle', 128],
[strChar, 'filepath', 128],
[strChar, 'filename', 64],
[strChar, 'acquire_timestamp', 32],
[strChar, 'header_timestamp', 32],
[strChar, 'save_timestamp', 32],
[strChar, 'file_comment', 512],
[strChar, 'reserve6', 96],
[strChar, 'dataset_comments', 512],
[strChar, 'user_data', 512]
]
pyFile = None
dictMarccd = None
try:
pyFile = open(_strFileName, "rb")
except:
EDVerbose.warning(
"EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: couldn't open file: "
+ _strFileName)
if (pyFile is not None):
EDVerbose.DEBUG(
"EDPluginExecReadImageHeaderMARCCDv10.readHeaderMarccd: Reading header from image "
+ _strFileName)
dictMarccd = {}
#Move to marccd part of header
pyFile.seek(1024)
for pyListRow in pyListHeader:
if len(pyListRow) == 3:
strFormat = str(pyListRow[2]) + str(pyListRow[0])
else:
strFormat = pyListRow[0]
strKeyword = pyListRow[1]
iReadSize = struct.calcsize(strFormat)
pyRawData = pyFile.read(iReadSize)
strValue = struct.unpack(strFormat, pyRawData)
if len(strValue) == 1:
strValue = strValue[0]
if pyListRow[0] == strChar:
strValue = strValue.strip('\x00')
dictMarccd[strKeyword] = strValue
pyFile.close()
return dictMarccd
