def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT" in self.__dictID11) and (self.__dictID11["DARK CURRENT"] == "YES") :
if ("DC FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"] == "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning("Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"] == "YES") :
if ("MASK FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"] == "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning("Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !" % (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(XSDataDouble(1 / value))
else:
self.warning("Asked for FF SCALE correction but no FF MULTIPLIER provided")
if ("SPATIAL DIS." in self.__dictID11) and (self.__dictID11["SPATIAL DIS."] == "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else :
self.warning("Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file")
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue((float(self.__dictID11["END AZIMUTH"]) - float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_1.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
# if strUnit is None: strUnit = "A"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
# if strUnit is None: strUnit = "mm"
# xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = xsd
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[") > 0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# xsd = XSDataAngle(float(strValue))
# if strUnit is None: strUnit = "deg"
# xsd.setUnit(XSDataString(strUnit))
# self.xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = xsd
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.edPluginPowderIntegration.executeSynchronous()
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(
self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(
self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT"
in self.__dictID11) and (self.__dictID11["DARK CURRENT"]
== "YES"):
if ("DC FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"]
== "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning(
"Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"]
== "YES"):
if ("MASK FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"]
== "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning(
"Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !"
% (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(
XSDataDouble(1 / value))
else:
self.warning(
"Asked for FF SCALE correction but no FF MULTIPLIER provided"
)
if ("SPATIAL DIS."
in self.__dictID11) and (self.__dictID11["SPATIAL DIS."]
== "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else:
self.warning(
"Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file"
)
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(
self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue(
(float(self.__dictID11["END AZIMUTH"]) -
float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(
XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsdOut = _edPlugin.getDataOutput()
if xsdOut is None:
strErr = "EDPluginControlDiffractionCTv1_2.doSuccessReadHeader: xsdataResult is None"
EDVerbose.ERROR(strErr)
self.setFailure()
raise RuntimeError(strErr)
xsDataDictionaryHeader = xsdOut.getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
lstValue = xsDataKeyValuePair.getValue().getValue().split()
if len(lstValue) == 2:
strValue = lstValue[0]
strUnit = lstValue[1]
else:
strValue = xsDataKeyValuePair.getValue().getValue()
strUnit = None
if (strKey == "_diffrn_radiation_wavelength"):
xsd = EDUtilsUnit.toXSD(XSDataWavelength, strValue)
self.xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(xsd)
elif (strKey == "_pd_instr_dist_spec/detc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(xsd)
elif (strKey == "_pd_meas_2theta_range_max"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(xsd)
elif (strKey == "_pd_meas_2theta_range_min"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(xsd)
elif (strKey == "_pd_meas_2theta_range_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(xsd)
elif (strKey == "_synchrotron_photon-flux"):
self.xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_scan_ampl(xsd)
elif (strKey == "_tomo_scan_type"):
self.xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(xsd)
elif (strKey == "_tomo_spec_displ_rotation_inc"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(xsd)
elif (strKey == "_tomo_spec_displ_x"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(xsd)
elif (strKey == "_tomo_spec_displ_x_inc"):
xsd = EDUtilsUnit.toXSD(XSDataLength, strValue)
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(xsd)
elif (strKey == "_tomo_spec_displ_x_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(xsd)
elif (strKey == "_tomo_spec_displ_x_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(xsd)
elif (strKey == "_tomo_spec_displ_z"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(xsd)
elif (strKey == "_tomo_spec_displ_z_inc"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(xsd)
elif (strKey == "_tomo_spec_displ_z_max"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(xsd)
elif (strKey == "_tomo_spec_displ_z_min"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(xsd)
elif (strKey == "_pd_instr_special_details_tilt_angle"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(xsd)
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
xsd = XSDataAngle(float(strValue))
if strUnit is None: strUnit = "deg"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(xsd)
elif (strKey == "_array_element_size[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_1(xsd)
elif (strKey == "_array_element_size[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "m"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_array_element_size_2(xsd)
elif (strKey == "_diffrn_detector_element.center[1]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(xsd)
elif (strKey == "_diffrn_detector_element.center[2]"):
xsd = XSDataLength(float(strValue))
if strUnit is None: strUnit = "mm"
xsd.setUnit(XSDataString(strUnit))
self.xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(xsd)
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
if self.xsdForceImageParam is not None:
self.forceImageParam(self.xsdForceImageParam)
if self.xsdForceScanParam is not None:
self.forceScanParam(self.xsdForceScanParam)
xsDataInputPowderIntegration.setImageParameters(self.xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.xsDataFileInputImage)
# Set the destination directory for output XRPD file
strDestinationDirectory = os.path.join(self.getDataInput().getDestinationDirectory().getPath().getValue(), \
self.getDataInput().getPowderDiffractionSubdirectory().getValue())
if self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() in ["flat", "spiral"]:
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_rotation_inc().getValue())
elif self.xsDataDiffractionCTInstrument.get_tomo_scan_type().getValue().lower() == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
pyintLineNumber = int(abs(self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z().getValue() - self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_min().getValue()) / self.xsDataDiffractionCTInstrument.get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
try:
strDestinationDirectory = "%s%04i" % (strDestinationDirectory, pyintLineNumber)
except TypeError:
pass #if pyintLineNumber is none: do not add suffix
xsDataInputPowderIntegration.setDestinationDir(XSDataFile(XSDataString(strDestinationDirectory)))
self.edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
