def testGenerateXSDataInputFIT2DCake(self):
strReferenceInputFile = os.path.join(self.m_strDataPath, "XSDataInputPowderDiffraction_reference.xml")
strXMLInput = EDUtilsTest.readAndParseFile(strReferenceInputFile)
EDApplication.loadModule("XSDataDiffractionCTv1")
from XSDataDiffractionCTv1 import XSDataInputPowderIntegration
xsDataInputPowderIntegration = XSDataInputPowderIntegration.parseString(strXMLInput)
from EDHandlerXSDataFIT2Dv1_0 import EDHandlerXSDataFIT2Dv1_0
edHandlerXSDataFIT2Dv1_0 = EDHandlerXSDataFIT2Dv1_0()
xsDataInputFIT2DCake = edHandlerXSDataFIT2Dv1_0.getXSDataInputFIT2DCake(xsDataInputPowderIntegration)
strReferencePath = os.path.join(self.m_strDataPath, "XSDataInputFIT2DCake_reference.xml")
strXMLInputReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDApplication.loadModule("XSDataFIT2Dv1_0")
from XSDataFIT2Dv1_0 import XSDataInputFIT2DCake
xsDataInputFIT2DCakeReference = XSDataInputFIT2DCake.parseString(strXMLInputReference)
EDAssert.equal(xsDataInputFIT2DCakeReference.marshal(), xsDataInputFIT2DCake.marshal())
def testGenerateXSDataInputFIT2DCake(self):
strReferenceInputFile = os.path.join(
self.m_strDataPath, "XSDataInputPowderDiffraction_reference.xml")
strXMLInput = EDUtilsTest.readAndParseFile(strReferenceInputFile)
EDApplication.loadModule("XSDataDiffractionCTv1")
from XSDataDiffractionCTv1 import XSDataInputPowderIntegration
xsDataInputPowderIntegration = XSDataInputPowderIntegration.parseString(
strXMLInput)
from EDHandlerXSDataFIT2Dv1_0 import EDHandlerXSDataFIT2Dv1_0
edHandlerXSDataFIT2Dv1_0 = EDHandlerXSDataFIT2Dv1_0()
xsDataInputFIT2DCake = edHandlerXSDataFIT2Dv1_0.getXSDataInputFIT2DCake(
xsDataInputPowderIntegration)
strReferencePath = os.path.join(self.m_strDataPath,
"XSDataInputFIT2DCake_reference.xml")
strXMLInputReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDApplication.loadModule("XSDataFIT2Dv1_0")
from XSDataFIT2Dv1_0 import XSDataInputFIT2DCake
xsDataInputFIT2DCakeReference = XSDataInputFIT2DCake.parseString(
strXMLInputReference)
EDAssert.equal(xsDataInputFIT2DCakeReference.marshal(),
xsDataInputFIT2DCake.marshal())
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput(
).getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if (strKey == "_diffrn_radiation_wavelength"):
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(
XSDataWavelength(float(strValue)))
elif (strKey == "_pd_instr_dist_spec/detc"):
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(
XSDataLength(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_max"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_min"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_inc"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_synchrotron_photon-flux"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(
XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(
XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_scan_type"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(
XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_rotation_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_x"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(
XSDataLength(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_angle"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_array_element_size[1]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_1(
XSDataLength(float(strValue)))
elif (strKey == "_array_element_size[2]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_2(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[1]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[2]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(
XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# 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.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# 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.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(
xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(
xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(
xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(
xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(
self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(
self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(
xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
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 testCheckParameters(self):
xsDataInput = XSDataInputPowderIntegration()
edPluginExecDCTPowderIntegration = self.createPlugin()
edPluginExecDCTPowderIntegration.setDataInput(xsDataInput)
edPluginExecDCTPowderIntegration.checkParameters()
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)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if strKey == "_diffrn_radiation_wavelength":
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(XSDataWavelength(float(strValue)))
elif strKey == "_pd_instr_dist_spec/detc":
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(XSDataLength(float(strValue)))
elif strKey == "_pd_meas_2theta_range_max":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_min":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_inc":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(XSDataAngle(float(strValue)))
elif strKey == "_synchrotron_photon-flux":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif strKey == "_synchrotron_ring-intensity":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif strKey == "_tomo_scan_ampl":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(XSDataAngle(float(strValue)))
elif strKey == "_tomo_scan_type":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif strKey == "_tomo_spec_displ_rotation":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_rotation_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_x":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(XSDataLength(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_angle":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(XSDataAngle(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_rotation":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(XSDataAngle(float(strValue)))
elif strKey == "_array_element_size[1]":
self.m_xsDataDiffractionCTImage.set_array_element_size_1(XSDataLength(float(strValue)))
elif strKey == "_array_element_size[2]":
self.m_xsDataDiffractionCTImage.set_array_element_size_2(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[1]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[2]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# 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.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# 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.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif strKey == "_file_correction_image_dark-current":
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif strKey == "_file_correction_image_flat-field":
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif strKey == "_file_correction_image-mask":
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif strKey == "_file_correction_spline_spatial-distortion":
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()