def preProcess(self, _edObject=None):
"""
The pre-process of ED Plugin Control DiffractionCT Powder Integration consists in preparing the input data for SPD Cake.
and declares the execution plugin as EDPluginFit2DCacke
"""
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("EDPluginControlDCTPowderIntegrationv1_1.preProcess")
# Load the execution plugin
self.m_edPluginPowderIntegration = self.loadPlugin(self.m_edStringControlledPluginName)
#Retrive its'datamodel
xsDataInputSPDCake = XSDataInputSPDCake()
instrumentParameters = self.getDataInput().getInstrumentParameters()
imageParameters = self.getDataInput().getImageParameters()
xsDataInputSPDCake.setInputFile(self.getDataInput().getImageFile())
xsDataInputSPDCake.setWavelength(instrumentParameters.get_diffrn_radiation_wavelength())
xsDataInputSPDCake.setSampleToDetectorDistance(instrumentParameters.get_pd_instr_dist_spec_detc())
xsDataInputSPDCake.setAngleOfTilt(imageParameters.get_pd_instr_special_details_tilt_angle())
xsDataInputSPDCake.setTiltRotation(imageParameters.get_pd_instr_special_details_tilt_rotation())
xsDataInputSPDCake.setDarkCurrentImageFile(imageParameters.get_file_correction_image_dark_current())
xsDataInputSPDCake.setFlatFieldImageFile(imageParameters.get_file_correction_image_flat_field())
xsDataInputSPDCake.setSpatialDistortionFile(imageParameters.get_file_correction_spline_spatial_distortion())
# EDVerbose.screen("imageParameters.get_array_element_size_1: %s" % imageParameters.get_array_element_size_1().marshal())
xsDataInputSPDCake.setBeamCentreInPixelsX(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_1()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_1())))
xsDataInputSPDCake.setBeamCentreInPixelsY(XSDataDouble(\
EDUtilsUnit.getSIValue(imageParameters.get_diffrn_detector_element_center_2()) / \
EDUtilsUnit.getSIValue(imageParameters.get_array_element_size_2())))
xsDataInputSPDCake.setPixelSizeX(imageParameters.get_array_element_size_1())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setPixelSizeY(imageParameters.get_array_element_size_2())
#imageParameters.get_diffrn_detector_element_center_1())
xsDataInputSPDCake.setBufferSizeX(XSDataInteger(2048))
xsDataInputSPDCake.setBufferSizeY(XSDataInteger(2048))
xsDataInputSPDCake.setStartAzimuth(XSDataAngle(0))
xsDataInputSPDCake.setStopAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setStepAzimuth(XSDataAngle(360))
xsDataInputSPDCake.setOutputDirCake(self.getDataInput().getDestinationDir())
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(True))
try:
self.m_edPluginPowderIntegration.setDataInput(xsDataInputSPDCake)
except Exception, error:
# This exception handling needs to be rethought, see bug #43.
errorMessage = EDMessage.ERROR_DATA_HANDLER_02 % ("EDPluginControlDCTPowderIntegrationv1_1.preProcess: Unexpected error in SPD handler: ", error)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
def unitTestGetValueAngle(self):
"""
Test conversion in length
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueAngle")
EDAssert.equal(
100.0,
EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataAngle, "90 deg"),
"grad"), "Length Conversion deg -> grad ")
def unitTestGetValueTime(self):
"""
Test conversion in Time
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueTime")
EDAssert.equal(
60.0,
EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataTime, "1 h"), "mn"),
"Length Conversion h -> mn ")
def unitTestGetValueLength(self):
"""
Test conversion in length
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueLength")
EDAssert.equal(
0.0452,
EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataLength, "45.2 um"),
"mm"), "Length Conversion um -> mm ")
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecNormalizeImagev1_2.preProcess")
sdi = self.getDataInput()
if sdi.dataScaleFactor is not None:
self.scaleData = sdi.dataScaleFactor.value
if sdi.darkScaleFactor is not None:
self.scaleDark = sdi.darkScaleFactor.value
if sdi.flatScaleFactor is not None:
self.scaleFlat = sdi.flatScaleFactor.value
if sdi.data == []:
strError = "You should either provide at least ONE input filename or an array, you provided: %s" % sdi.marshal()
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
else:
for inputData in sdi.data:
if inputData.exposureTime is None:
self.WARNING("You did not provide an exposure time for DATA... using default: 1")
self.listDataExposure.append(1.0)
else:
self.listDataExposure.append(EDUtilsUnit.getSIValue(inputData.exposureTime))
self.listDataArray.append(EDUtilsArray.getArray(inputData) / self.scaleData)
for inputFlat in sdi.flat:
if inputFlat.exposureTime is None:
self.WARNING("You did not provide an exposure time for FLAT... using default: 1")
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputFlat.exposureTime)
self.listFlatExposure.append(expTime)
self.listFlatArray.append(EDUtilsArray.getArray(inputFlat) / self.scaleFlat)
with self.__class__.semaphore:
for inputDark in sdi.dark:
if inputDark.exposureTime is None:
self.WARNING("You did not provide an exposure time for Dark... using default: 1")
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputDark.exposureTime)
# strMeanDarkKey = "/".join((self.getClassName(), "MeanDark%6.3f" % expTime))
if str(expTime) not in self.__class__.dictDark:
self.listDarkExposure.append(expTime)
self.listDarkArray.append(EDUtilsArray.getArray(inputDark) / self.scaleDark)
if sdi.output is not None:
if (sdi.output.path is not None):
self.strOutputFilename = sdi.output.path.value
elif (sdi.output.shared is not None):
self.strOutputShared = sdi.output.shared.value
# else export as array.
EDAssert.equal(len(self.listDataArray), len(self.listDataExposure), _strComment="number of data images / exposure times ")
EDAssert.equal(len(self.listFlatArray), len(self.listFlatExposure), _strComment="number of flat images / exposure times ")
EDAssert.equal(len(self.listDarkArray), len(self.listDarkExposure), _strComment="number of dark images / exposure times ")
def unitTestGetSIValue(self):
"""
test the execution of unitTestGetSIValue static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetSIValue")
xsd = XSDataLength(1.5)
xsd.setUnit(XSDataString("mm"))
EDAssert.equal(0.0015, EDUtilsUnit.getSIValue(xsd), "Conversion mm to meter")
xsd = XSDataAngle(90)
xsd.setUnit(XSDataString("deg"))
EDAssert.equal(math.pi / 2, EDUtilsUnit.getSIValue(xsd), "Conversion deg to rad")
def unitTestGetSIValue(self):
"""
test the execution of unitTestGetSIValue static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetSIValue")
xsd = XSDataLength(1.5)
xsd.setUnit(XSDataString("mm"))
EDAssert.equal(0.0015, EDUtilsUnit.getSIValue(xsd),
"Conversion mm to meter")
xsd = XSDataAngle(90)
xsd.setUnit(XSDataString("deg"))
EDAssert.equal(math.pi / 2, EDUtilsUnit.getSIValue(xsd),
"Conversion deg to rad")
def getDetector(xsDetector):
detector = None
if xsDetector.name and (xsDetector.name.value in dir(pyFAI.detectors)):
detector = getattr(pyFAI.detectors, xsDetector.name.value)()
else:
pixel2 = EDUtilsUnit.getSIValue(xsDetector.pixelSizeX)
pixel1 = EDUtilsUnit.getSIValue(xsDetector.pixelSizeY)
if xsDetector.splineFile and os.path.isFile(xsDetector.splineFile.path.value):
dictGeo = {"pixel1":pixel1, "pixel2":pixel2, "splineFile":xsDetector.splineFile.path.value}
else:
dictGeo = {"pixel1":pixel1, "pixel2":pixel2, "splineFile":None}
detector = pyFAI.detectors.Detector()
detector.setPyFAI(**dictGeo)
return detector
def getDetector(xsDetector):
detector = None
if xsDetector.name and (xsDetector.name.value in dir(pyFAI.detectors)):
detector = getattr(pyFAI.detectors, xsDetector.name.value)()
else:
pixel2 = EDUtilsUnit.getSIValue(xsDetector.pixelSizeX)
pixel1 = EDUtilsUnit.getSIValue(xsDetector.pixelSizeY)
if xsDetector.splineFile and os.path.isFile(xsDetector.splineFile.path.value):
dictGeo = {"pixel1":pixel1, "pixel2":pixel2, "splineFile":xsDetector.splineFile.path.value}
else:
dictGeo = {"pixel1":pixel1, "pixel2":pixel2, "splineFile":None}
detector = pyFAI.detectors.Detector()
detector.setPyFAI(**dictGeo)
return detector
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecPyFAIv1_0.preProcess")
sdi = self.dataInput
ai = pyFAI.AzimuthalIntegrator()
if sdi.geometryFit2D is not None:
xsGeometry = sdi.geometryFit2D
detector = self.getDetector(xsGeometry.detector)
d = {"direct": EDUtilsUnit.getSIValue(xsGeometry.distance) * 1000, #fit2D takes the distance in mm
"centerX": xsGeometry.beamCentreInPixelsX.value ,
"centerY":xsGeometry.beamCentreInPixelsY.value ,
"tilt": xsGeometry.angleOfTilt.value,
"tiltPlanRotation": xsGeometry.tiltRotation.value}
d.update(detector.getFit2D())
ai.setFit2D(**d)
elif sdi.geometryPyFAI is not None:
xsGeometry = sdi.geometryPyFAI
detector = self.getDetector(xsGeometry.detector)
d = {"dist": EDUtilsUnit.getSIValue(xsGeometry.sampleDetectorDistance),
"poni1": EDUtilsUnit.getSIValue(xsGeometry.pointOfNormalIncidence1),
"poni2": EDUtilsUnit.getSIValue(xsGeometry.pointOfNormalIncidence2),
"rot1": EDUtilsUnit.getSIValue(xsGeometry.rotation1),
"rot2": EDUtilsUnit.getSIValue(xsGeometry.rotation2),
"rot3": EDUtilsUnit.getSIValue(xsGeometry.rotation3)}
d.update(detector.getPyFAI())
ai.setPyFAI(**d)
else:
strError = "Geometry definition in %s, not recognized as a valid geometry%s %s" % (sdi, os.linesep, sdi.marshal())
self.ERROR(strError)
raise RuntimeError(strError)
########################################################################
# Choose the azimuthal integrator
########################################################################
with self.__class__._sem:
if tuple(ai.param) in self.__class__._dictGeo:
self.ai = self.__class__._dictGeo[tuple(ai.param)]
else:
self.__class__._dictGeo[tuple(ai.param)] = ai
self.ai = ai
self.data = EDUtilsArray.getArray(self.dataInput.input).astype(float)
if sdi.dark is not None:
self.data -= EDUtilsArray.getArray(sdi.dark)
if sdi.flat is not None:
self.data /= EDUtilsArray.getArray(sdi.flat)
if sdi.mask is not None:
self.mask = EDUtilsArray.getArray(sdi.mask)
if sdi.wavelength is not None:
self.ai.wavelength = EDUtilsUnit.getSIValue(sdi.wavelength)
if sdi.output is not None:
self.strOutputFile = sdi.output.path.value
if sdi.dummy is not None:
self.dummy = sdi.dummy.value
if sdi.deltaDummy is not None:
self.delta_dummy = sdi.deltaDummy.value
if sdi.nbPt:
self.nbPt = sdi.nbPt.value
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecPyFAIv1_0.preProcess")
sdi = self.dataInput
ai = pyFAI.AzimuthalIntegrator()
if sdi.geometryFit2D is not None:
xsGeometry = sdi.geometryFit2D
detector = self.getDetector(xsGeometry.detector)
d = {"direct": EDUtilsUnit.getSIValue(xsGeometry.distance) * 1000, #fit2D takes the distance in mm
"centerX": xsGeometry.beamCentreInPixelsX.value ,
"centerY":xsGeometry.beamCentreInPixelsY.value ,
"tilt": xsGeometry.angleOfTilt.value,
"tiltPlanRotation": xsGeometry.tiltRotation.value}
d.update(detector.getFit2D())
ai.setFit2D(**d)
elif sdi.geometryPyFAI is not None:
xsGeometry = sdi.geometryPyFAI
detector = self.getDetector(xsGeometry.detector)
d = {"dist": EDUtilsUnit.getSIValue(xsGeometry.sampleDetectorDistance),
"poni1": EDUtilsUnit.getSIValue(xsGeometry.pointOfNormalIncidence1),
"poni2": EDUtilsUnit.getSIValue(xsGeometry.pointOfNormalIncidence2),
"rot1": EDUtilsUnit.getSIValue(xsGeometry.rotation1),
"rot2": EDUtilsUnit.getSIValue(xsGeometry.rotation2),
"rot3": EDUtilsUnit.getSIValue(xsGeometry.rotation3)}
d.update(detector.getPyFAI())
ai.setPyFAI(**d)
else:
strError = "Geometry definition in %s, not recognized as a valid geometry%s %s" % (sdi, os.linesep, sdi.marshal())
self.ERROR(strError)
raise RuntimeError(strError)
########################################################################
# Choose the azimuthal integrator
########################################################################
with self.__class__._sem:
if tuple(ai.param) in self.__class__._dictGeo:
self.ai = self.__class__._dictGeo[tuple(ai.param)]
else:
self.__class__._dictGeo[tuple(ai.param)] = ai
self.ai = ai
self.data = EDUtilsArray.getArray(self.dataInput.input).astype(float)
if sdi.dark is not None:
self.data -= EDUtilsArray.getArray(sdi.dark)
if sdi.flat is not None:
self.data /= EDUtilsArray.getArray(sdi.flat)
if sdi.mask is not None:
self.mask = EDUtilsArray.getArray(sdi.mask)
if sdi.wavelength is not None:
self.ai.wavelength = EDUtilsUnit.getSIValue(sdi.wavelength)
if sdi.output is not None:
self.strOutputFile = sdi.output.path.value
if sdi.dummy is not None:
self.dummy = sdi.dummy.value
if sdi.deltaDummy is not None:
self.delta_dummy = sdi.deltaDummy.value
if sdi.nbPt:
self.nbPt = sdi.nbPt.value
def getInputParameter(self):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCakev1_5.getInputParameter")
EDPluginSPDCorrectv10.getInputParameter(self)
if self.xsDataInputSPD.getStartAzimuth() is not None:
if self.xsDataInputSPD.getStartAzimuth().getUnit() is not None:
self.dictGeometry["StartAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStartAzimuth(), "deg")
else:
self.WARNING("You did not specify the StartAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StartAzimuth"] = self.xsDataInputSPD.getStartAzimuth().getValue()
if self.xsDataInputSPD.getStopAzimuth() is not None:
if self.xsDataInputSPD.getStopAzimuth().getUnit() is not None:
self.dictGeometry["StopAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStopAzimuth(), "deg")
else:
self.WARNING("You did not specify the StopAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StopAzimuth"] = self.xsDataInputSPD.getStopAzimuth().getValue()
if self.xsDataInputSPD.getStepAzimuth() is not None:
if self.xsDataInputSPD.getStepAzimuth().getUnit() is not None:
self.dictGeometry["StepAzimuth"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getStepAzimuth(), "deg")
else:
self.WARNING("You did not specify the StepAzimuth Unit, Falling back to Deg (not Rad)")
self.dictGeometry["StepAzimuth"] = self.xsDataInputSPD.getStepAzimuth().getValue()
if self.xsDataInputSPD.getInnerRadius() is not None:
self.dictGeometry["InnerRadius"] = self.xsDataInputSPD.getInnerRadius().getValue()
if self.xsDataInputSPD.getOuterRadius() is not None:
self.dictGeometry["OuterRadius"] = self.xsDataInputSPD.getOuterRadius().getValue()
if self.xsDataInputSPD.getOutputDirCake() is not None:
self.dictGeometry["OutputDirCake"] = self.xsDataInputSPD.getOutputDirCake().getPath().getValue()
EDUtilsPath.createFolder(self.dictGeometry["OutputDirCake"])
if self.dictGeometry["OutputDirCake"] != self.dictGeometry["OutputDir"]:
self.setFireAndForget(False)
else:
self.dictGeometry["OutputDirCake"] = self.dictGeometry["OutputDir"]
if self.xsDataInputSPD.getMaskFile() is not None:
self.dictGeometry["MaskFile"] = self.xsDataInputSPD.getMaskFile().getPath().getValue()
if not os.path.isfile(self.dictGeometry["MaskFile"]):
self.ERROR("Mask file %s does not exist " % self.dictGeometry["MaskFile"])
self.dictGeometry.pop("MaskFile")
if self.xsDataInputSPD.getIntensityScaleFactor() is not None:
self.dictGeometry["IntensityScaleFactor"] = self.xsDataInputSPD.getIntensityScaleFactor().getValue()
if self.xsDataInputSPD.getDeleteCorImg() is not None:
self.bDeleteCorImg = (self.xsDataInputSPD.getDeleteCorImg().getValue() in ["1", 1, "true", "True", True])
if self.bDeleteCorImg:
self.setFireAndForget(False)
if self.xsDataInputSPD.getCorrectTiltMask() is not None:
self.bCorrectTiltMask = bool(self.xsDataInputSPD.getCorrectTiltMask().getValue())
def integrate(self):
img = fabio.open(self.rawImage)
if "Date" in img.header:
self.experimentSetup.timeOfFrame = XSDataTime(time.mktime(time.strptime(img.header["Date"], "%a %b %d %H:%M:%S %Y")))
wavelength = EDUtilsUnit.getSIValue(self.experimentSetup.wavelength)
current_config = self.integrator.getPyFAI()
short_config = {}
for key in self.integrator_config:
short_config[key] = current_config[key]
with self.__class__.semaphore:
if (short_config != self.integrator_config) or \
(self.integrator.wavelength != wavelength) or\
(self.maskfile != self.experimentSetup.maskFile.path.value):
self.screen("Resetting PyFAI integrator")
self.integrator.setPyFAI(**self.integrator_config)
self.integrator.wavelength = wavelength
self.integrator.detector.mask = self.calc_mask()
q, I, std = self.integrator.integrate1d(data=img.data, nbPt=max(img.dim1, img.dim2),
correctSolidAngle=True,
dummy=self.dummy, delta_dummy=self.delta_dummy,
filename=None,
error_model="poisson",
radial_range=None, azimuth_range=None,
polarization_factor=0, dark=None, flat=None,
method=self.METHOD, unit="q_nm^-1", safe=False)
self.lstExecutiveSummary.append("Azimuthal integration of raw image '%s'-->'%s'." % (self.rawImage, self.integratedCurve))
return q, I, std
def unitTestGetValueSIAngle(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSIAngle")
EDAssert.equal(math.pi / 2.0, EDUtilsUnit.getValueAngle(90, "deg"),
"Angle Conversion deg -> rad ")
def integrate(self):
img = fabio.open(self.rawImage)
if "Date" in img.header:
self.experimentSetup.timeOfFrame = XSDataTime(time.mktime(time.strptime(img.header["Date"], "%a %b %d %H:%M:%S %Y")))
wavelength = EDUtilsUnit.getSIValue(self.experimentSetup.wavelength)
current_config = self.integrator.getPyFAI()
short_config = {}
for key in self.integrator_config:
short_config[key] = current_config[key]
with self.__class__.semaphore:
if (short_config != self.integrator_config) or \
(self.integrator.wavelength != wavelength) or\
(self.maskfile != self.experimentSetup.maskFile.path.value):
self.screen("Resetting PyFAI integrator")
self.integrator.setPyFAI(**self.integrator_config)
self.integrator.wavelength = wavelength
self.integrator.detector.mask = self.calc_mask()
q, I, std = self.integrator.integrate1d(img.data, max(img.dim1, img.dim2),
correctSolidAngle=True,
dummy=self.dummy, delta_dummy=self.delta_dummy,
filename=None,
error_model="poisson",
radial_range=None, azimuth_range=None,
polarization_factor=0, dark=None, flat=None,
method=self.METHOD, unit="q_nm^-1", safe=False)
self.lstExecutiveSummary.append("Azimuthal integration of raw image '%s'-->'%s'." % (self.rawImage, self.integratedCurve))
return q, I, std
def unitTestGetValueSILength(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSILength")
EDAssert.equal(1.54E-10, EDUtilsUnit.getValueLength(1.54, "A"),
"Length Conversion A -> m ")
def integrate(self):
#with fabio.fabioutils.File(self.rawImage) as raw:
img = fabio.open(self.rawImage)
number_of_bins = self.number_of_bins or max(img.dim1, img.dim2)
if "Date" in img.header:
self.experimentSetup.timeOfFrame = XSDataTime(time.mktime(time.strptime(img.header["Date"], "%a %b %d %H:%M:%S %Y")))
new_integrator = pyFAI.AzimuthalIntegrator(detector=self.detector)
new_integrator.setFit2D(self.experimentSetup.detectorDistance.value * 1000,
self.experimentSetup.beamCenter_1.value,
self.experimentSetup.beamCenter_2.value)
new_integrator.wavelength = EDUtilsUnit.getSIValue(self.experimentSetup.wavelength)
with self.__class__.semaphore:
if (str(new_integrator) != str(self.integrator) or
self.maskfile != self.experimentSetup.maskFile.path.value):
self.screen("Resetting PyFAI integrator")
new_integrator.detector.mask = self.calc_mask()
self.__class__.integrator = new_integrator
res_tuple = self.integrator.integrate1d(img.data, number_of_bins,
correctSolidAngle=True,
dummy=self.dummy, delta_dummy=self.delta_dummy,
filename=None,
error_model="poisson",
radial_range=None, azimuth_range=None,
polarization_factor=0.99, dark=None, flat=None,
method=self.METHOD, unit="q_nm^-1", safe=False,
normalization_factor=self.normalization_factor
)
self.lstExecutiveSummary.append("Azimuthal integration of raw image '%s'-->'%s'." % (self.rawImage, self.integratedCurve))
return res_tuple
def unitTestGetValueSITime(self):
"""
Test sub method specific to length: GetValueTime
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSITime")
EDAssert.equal(1800, EDUtilsUnit.getValueTime(30, "mn"),
"Length Conversion mn -> s ")
def unitTestToXSD(self):
"""
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestToXSD")
xsdObt = EDUtilsUnit.toXSD(XSDataLength, "1.5 mm")
xsdExp = XSDataLength(1.5)
xsdExp.setUnit(XSDataString("mm"))
EDAssert.equal(xsdExp.marshal(), xsdObt.marshal(), "XML representation are the same")
def unitTestToXSD(self):
"""
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestToXSD")
xsdObt = EDUtilsUnit.toXSD(XSDataLength, "1.5 mm")
xsdExp = XSDataLength(1.5)
xsdExp.setUnit(XSDataString("mm"))
EDAssert.equal(xsdExp.marshal(), xsdObt.marshal(),
"XML representation are the same")
def integrate(self):
#with fabio.fabioutils.File(self.rawImage) as raw:
img = fabio.open(self.rawImage)
number_of_bins = self.number_of_bins or max(img.dim1, img.dim2)
if "Date" in img.header:
self.experimentSetup.timeOfFrame = XSDataTime(
time.mktime(
time.strptime(img.header["Date"], "%a %b %d %H:%M:%S %Y")))
new_integrator = pyFAI.AzimuthalIntegrator(detector=self.detector)
new_integrator.setFit2D(
self.experimentSetup.detectorDistance.value * 1000,
self.experimentSetup.beamCenter_1.value,
self.experimentSetup.beamCenter_2.value)
new_integrator.wavelength = EDUtilsUnit.getSIValue(
self.experimentSetup.wavelength)
with self.__class__.semaphore:
if (str(new_integrator) != str(self.integrator) or
self.maskfile != self.experimentSetup.maskFile.path.value):
self.screen("Resetting PyFAI integrator")
new_integrator.detector.mask = self.calc_mask()
self.__class__.integrator = new_integrator
res_tuple = self.integrator.integrate1d(
img.data,
number_of_bins,
correctSolidAngle=True,
dummy=self.dummy,
delta_dummy=self.delta_dummy,
filename=None,
error_model="poisson",
radial_range=None,
azimuth_range=None,
polarization_factor=0.99,
dark=None,
flat=None,
method=self.METHOD,
unit="q_nm^-1",
safe=False,
normalization_factor=self.normalization_factor)
self.lstExecutiveSummary.append(
"Azimuthal integration of raw image '%s'-->'%s'." %
(self.rawImage, self.integratedCurve))
valid_bins = abs(res_tuple.intensity - self.dummy) > self.delta_dummy
short_tuple = res_tuple.__class__(res_tuple.radial[valid_bins],
res_tuple.intensity[valid_bins],
res_tuple.sigma[valid_bins])
return short_tuple
def unitTestGetValueSITime(self):
"""
Test sub method specific to length: GetValueTime
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSITime")
EDAssert.equal(1800, EDUtilsUnit.getValueTime(30, "mn"), "Length Conversion mn -> s ")
def unitTestGetValueLength(self):
"""
Test conversion in length
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueLength")
EDAssert.equal(0.0452, EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataLength, "45.2 um"), "mm"), "Length Conversion um -> mm ")
def unitTestGetValueSILength(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSILength")
EDAssert.equal(1.54E-10, EDUtilsUnit.getValueLength(1.54, "A"), "Length Conversion A -> m ")
def unitTestGetValueSIAngle(self):
"""
Test sub method specific to length: GetValueLength
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueSIAngle")
EDAssert.equal(math.pi / 2.0, EDUtilsUnit.getValueAngle(90, "deg"), "Angle Conversion deg -> rad ")
def getInputParameter(self, _edObject=None):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCorrectv10.getInputParameter")
self.xsDataInputSPD = self.getDataInput()
self.pathToInputFile = self.xsDataInputSPD.getInputFile().getPath().getValue()
if not os.path.isfile(self.pathToInputFile):
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
self.pathToInputFile,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getDarkCurrentImageFile() is not None:
pathToDarkCurrentImageFile = self.xsDataInputSPD.getDarkCurrentImageFile().getPath().getValue()
if os.path.isfile(pathToDarkCurrentImageFile):
self.dictGeometry["DarkCurrentImageFile"] = pathToDarkCurrentImageFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDarkCurrentImageFile,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getFlatFieldImageFile() is not None:
pathToFlatFieldImageFile = self.xsDataInputSPD.getFlatFieldImageFile().getPath().getValue()
if os.path.isfile(pathToFlatFieldImageFile):
self.dictGeometry["FlatFieldImageFile"] = pathToFlatFieldImageFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToFlatFieldImageFile,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getSpatialDistortionFile() is not None:
pathToSpatialDistortionFile = self.xsDataInputSPD.getSpatialDistortionFile().getPath().getValue()
if os.path.isfile(pathToSpatialDistortionFile):
self.dictGeometry["SpatialDistortionFile"] = pathToSpatialDistortionFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToSpatialDistortionFile,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getAngleOfTilt() is not None:
if self.xsDataInputSPD.getAngleOfTilt().getUnit() is not None:
self.dictGeometry["AngleOfTilt"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getAngleOfTilt(), "deg")
else: # Fall-back by default to deg
self.WARNING("You did not specify the AngleOfTilt unit ... I Guess it is deg")
self.dictGeometry["AngleOfTilt"] = self.xsDataInputSPD.getAngleOfTilt().getValue()
else:
self.dictGeometry["AngleOfTilt"] = 0
if self.xsDataInputSPD.getTiltRotation() is not None:
if self.xsDataInputSPD.getTiltRotation().getUnit() is not None:
self.dictGeometry["TiltRotation"] = EDUtilsUnit.getValue(self.xsDataInputSPD.getTiltRotation(), "deg")
else: # Fall-back by default to deg
self.WARNING("You did not specify the TiltRotation unit ... I Guess it is deg")
self.dictGeometry["TiltRotation"] = self.xsDataInputSPD.getTiltRotation().getValue()
else:
self.dictGeometry["TiltRotation"] = 0
if self.xsDataInputSPD.getBeamCentreInPixelsX() is not None:
self.dictGeometry["BeamCenterX"] = self.xsDataInputSPD.getBeamCentreInPixelsX().getValue()
if self.xsDataInputSPD.getBeamCentreInPixelsY() is not None:
self.dictGeometry["BeamCenterY"] = self.xsDataInputSPD.getBeamCentreInPixelsY().getValue()
if self.xsDataInputSPD.getBufferSizeX() is not None:
self.dictGeometry["BufferSizeX"] = self.xsDataInputSPD.getBufferSizeX().getValue()
if self.xsDataInputSPD.getBufferSizeY() is not None:
self.dictGeometry["BufferSizeY"] = self.xsDataInputSPD.getBufferSizeY().getValue()
if self.xsDataInputSPD.getDistortionFileX() is not None:
pathToDistortionFileX = self.xsDataInputSPD.getDistortionFileX().getPath().getValue()
if os.path.isfile(pathToDistortionFileX):
self.dictGeometry["DistortionFileX"] = pathToDistortionFileX
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDistortionFileX,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getDistortionFileY() is not None:
pathToDistortionFileY = self.xsDataInputSPD.getDistortionFileY().getPath().getValue()
if os.path.isfile(pathToDistortionFileY):
self.dictGeometry["DistortionFileY"] = pathToDistortionFileY
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDistortionFileY,
)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getPixelSizeX() is not None:
self.dictGeometry["PixelSizeX"] = EDUtilsUnit.getSIValue(self.xsDataInputSPD.getPixelSizeX())
if self.xsDataInputSPD.getPixelSizeY() is not None:
self.dictGeometry["PixelSizeY"] = EDUtilsUnit.getSIValue(self.xsDataInputSPD.getPixelSizeY())
if self.xsDataInputSPD.getSampleToDetectorDistance() is not None:
self.dictGeometry["SampleToDetectorDistance"] = EDUtilsUnit.getSIValue(
self.xsDataInputSPD.getSampleToDetectorDistance()
)
if self.xsDataInputSPD.getWavelength() is not None:
if self.xsDataInputSPD.getWavelength().getUnit() is not None:
self.dictGeometry["Wavelength"] = EDUtilsUnit.getSIValue(self.xsDataInputSPD.getWavelength())
else: # Fall-back to Angsrom
self.WARNING("You did not specify the wavelength unit ... I Guess it is Angstrom")
self.dictGeometry["Wavelength"] = self.xsDataInputSPD.getWavelength().getValue() * 1e-10
if self.xsDataInputSPD.getOutputFileType() is not None:
self.dictGeometry["OutputFileType"] = self.xsDataInputSPD.getOutputFileType().getValue()
if not self.dictGeometry["OutputFileType"].startswith("."):
self.dictGeometry["OutputFileType"] = "." + self.dictGeometry["OutputFileType"]
else:
self.dictGeometry["OutputFileType"] = ".edf"
if self.xsDataInputSPD.getOutputDir() is not None:
tmpdir = self.xsDataInputSPD.getOutputDir().getPath().getValue()
if os.path.isdir(tmpdir):
self.dictGeometry["OutputDir"] = tmpdir
if tmpdir != os.path.dirname(self.pathToInputFile):
self._bFireAndForget = True
else:
self.WARNING(
"The destination directory %s does not exist, using working directory instead %s"
% (tmpdir, self.getWorkingDirectory())
)
self.dictGeometry["OutputDir"] = self.getWorkingDirectory()
else:
self.dictGeometry["OutputDir"] = os.path.dirname(self.pathToInputFile)
if (
self.dictGeometry["OutputDir"] == os.path.dirname(self.pathToInputFile)
and not (self.pathToInputFile.endswith(self.dictGeometry["OutputFileType"]))
and not (self.dictGeometry["OutputFileType"].lower() in [".h5", ".chi", ".nx", ".nexus", ".cif"])
):
self.bFireAndForget = True
def readArrayFromFile(self, _filename):
"""
Populate self.inputArray for a given filename and extracts as well
self.fPixelSize
self.fDistance
self.fRadOffset
self.wavelength ...
"""
image = openimage(_filename)
self.inputArray = image.data
self.dHeader = image.header
if "Offset_1" in self.dHeader:
offset, unit = self.dHeader["Offset_1"].split(None, 1)
if unit.lower() != "pixel":
EDVerbose.WARNING(
"I got a strange unit for offset: %s, I expected pixel." %
self.dHeader["Offset_1"])
try:
self.fRadOffset = float(offset)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize this offset and convert it to float: %s" % self.dHeader[
"Offset_1"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if "Offset_2" in self.dHeader:
offset, unit = self.dHeader["Offset_2"].split(None, 1)
if unit.lower() != "pixel":
EDVerbose.WARNING(
"I got a strange unit for offset: %s, I expected pixel." %
self.dHeader["Offset_2"])
try:
self.fAzimOffset = float(offset)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize this offset and convert it to float: %s" % self.dHeader[
"Offset_2"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if "PSize_1" in self.dHeader:
psize, unit = self.dHeader["PSize_1"].split(None, 1)
try:
fPixelSize = float(psize)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the radial pixel size and convert it to float: %s" % self.dHeader[
"PSize_1"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.fPixelSize = EDUtilsUnit.getValueLength(fPixelSize, unit)
if "PSize_2" in self.dHeader:
psize, unit = self.dHeader["PSize_2"].split(None, 1)
try:
fPixelSize = float(psize)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the azimuthal pixel size and convert it to float: %s" % self.dHeader[
"PSize_2"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.fAzimSize = EDUtilsUnit.getValueAngle(fPixelSize, unit)
if ("SampleDistance" in self.dHeader):
distance, unit = self.dHeader["SampleDistance"].split(None, 1)
try:
fDistance = float(distance)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the Sample Distance is and convert it to float: %s" % self.dHeader[
"SampleDistance"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
self.fDistance = EDUtilsUnit.getValueLength(fDistance, unit)
if ("WaveLength" in self.dHeader):
wavelenth, unit = self.dHeader["WaveLength"].split(None, 1)
try:
fWavelength = float(wavelenth)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the wavelength is and convert it to float: %s" % self.dHeader[
"WaveLength"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
self.fWavelength = EDUtilsUnit.getValueLength(fWavelength, unit)
if ("Dummy" in self.dHeader):
self.fDummy = float(self.dHeader.get("Dummy", 0))
if ("DDummy" in self.dHeader):
self.fDeltaDummy = float(self.dHeader.get("DDummy", 0.1))
def unitTestGetValueAngle(self):
"""
Test conversion in length
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueAngle")
EDAssert.equal(100.0, EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataAngle, "90 deg"), "grad"), "Length Conversion deg -> grad ")
def preProcess(self, _edObject=None):
"""
Preprocess: check the input parameters and unpack them
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginExportAsciiPowderv1_0.preProcess")
if self.getDataInput().getEdfFile() is not None:
self.inputFilename = self.getDataInput().getEdfFile().getPath(
).getValue()
if not os.path.isfile(self.inputFilename):
EDVerbose.ERROR(
"The input file provided is not a valid file: %s" %
self.inputFilename)
raise RuntimeError("Not a valid file %s" % self.inputFilename)
else:
self.readArrayFromFile(self.inputFilename)
elif self.getDataInput().getIntensities() is not None:
self.inputArray = EDUtilsArray.xsDataToArray(
self.getDataInput().getIntensities())
else:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.preProcess: neither an input image, neither a data array given in input !"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if self.getDataInput().getDistance() is not None:
self.fDistance = EDUtilsUnit.getSIValue(
self.getDataInput().getDistance())
if self.getDataInput().getPixelSize() is not None:
self.fPixelSize = EDUtilsUnit.getSIValue(
self.getDataInput().getPixelSize())
if self.getDataInput().getOffset() is not None:
self.fRadOffset = self.getDataInput().getOffset().getValue()
if self.getDataInput().getOutputFormat() is not None:
self.strFormat = self.getDataInput().getOutputFormat().getValue(
).lower()
if self.getDataInput().getNumberOfBins() is not None:
self.iNbBins = self.getDataInput().getNumberOfBins().getValue()
if self.strFormat == "array":
self.outputFilename = None
else:
if self.getDataInput().getOutputFile() is None:
if "chi" in self.strFormat:
ext = ".chi"
elif "cif" in self.strFormat:
ext = ".cif"
elif "spr" in self.strFormat:
ext = ".spr"
else:
ext = ".powder"
self.outputFilename = os.path.join(self.getWorkingDirectory(),
"output" + ext)
else:
self.outputFilename = self.getDataInput().getOutputFile(
).getPath().getValue()
if os.path.isdir(self.outputFilename):
if "chi" in self.strFormat:
ext = ".chi"
elif "cif" in self.strFormat:
ext = ".cif"
elif "spr" in self.strFormat:
ext = ".spr"
else:
ext = ".powder"
self.outputFilename = os.path.join(
self.outputFilename,
os.path.splitext(os.path.basename(
self.inputFilename))[0] + ext)
if (self.fPixelSize is None) or (self.fDistance is None):
strErrorMessage = "EDPluginExportAsciiPowderv1_0.preProcess: pixel size: %s; distance: %s Cannot be identified in %s !!!!" % (
self.fPixelSize, self.fDistance, self.inputFilename)
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecNormalizeImagev1_2.preProcess")
sdi = self.getDataInput()
if sdi.dataScaleFactor is not None:
self.scaleData = sdi.dataScaleFactor.value
if sdi.darkScaleFactor is not None:
self.scaleDark = sdi.darkScaleFactor.value
if sdi.flatScaleFactor is not None:
self.scaleFlat = sdi.flatScaleFactor.value
if sdi.data == []:
strError = "You should either provide at least ONE input filename or an array, you provided: %s" % sdi.marshal(
)
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
else:
for inputData in sdi.data:
if inputData.exposureTime is None:
self.WARNING(
"You did not provide an exposure time for DATA... using default: 1"
)
self.listDataExposure.append(1.0)
else:
self.listDataExposure.append(
EDUtilsUnit.getSIValue(inputData.exposureTime))
self.listDataArray.append(
EDUtilsArray.getArray(inputData) / self.scaleData)
for inputFlat in sdi.flat:
if inputFlat.exposureTime is None:
self.WARNING(
"You did not provide an exposure time for FLAT... using default: 1"
)
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputFlat.exposureTime)
self.listFlatExposure.append(expTime)
self.listFlatArray.append(
EDUtilsArray.getArray(inputFlat) / self.scaleFlat)
with self.__class__.semaphore:
for inputDark in sdi.dark:
if inputDark.exposureTime is None:
self.WARNING(
"You did not provide an exposure time for Dark... using default: 1"
)
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputDark.exposureTime)
# strMeanDarkKey = "/".join((self.getClassName(), "MeanDark%6.3f" % expTime))
if str(expTime) not in self.__class__.dictDark:
self.listDarkExposure.append(expTime)
self.listDarkArray.append(
EDUtilsArray.getArray(inputDark) / self.scaleDark)
if sdi.output is not None:
if (sdi.output.path is not None):
self.strOutputFilename = sdi.output.path.value
elif (sdi.output.shared is not None):
self.strOutputShared = sdi.output.shared.value
# else export as array.
EDAssert.equal(len(self.listDataArray),
len(self.listDataExposure),
_strComment="number of data images / exposure times ")
EDAssert.equal(len(self.listFlatArray),
len(self.listFlatExposure),
_strComment="number of flat images / exposure times ")
EDAssert.equal(len(self.listDarkArray),
len(self.listDarkExposure),
_strComment="number of dark images / exposure times ")
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 getInputParameter(self, _edObject=None):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCorrectv10.getInputParameter")
self.xsDataInputSPD = self.getDataInput()
self.pathToInputFile = self.xsDataInputSPD.getInputFile().getPath(
).getValue()
if not os.path.isfile(self.pathToInputFile):
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess", self.pathToInputFile)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getDarkCurrentImageFile() is not None:
pathToDarkCurrentImageFile = self.xsDataInputSPD.getDarkCurrentImageFile(
).getPath().getValue()
if os.path.isfile(pathToDarkCurrentImageFile):
self.dictGeometry[
"DarkCurrentImageFile"] = pathToDarkCurrentImageFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDarkCurrentImageFile)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getFlatFieldImageFile() is not None:
pathToFlatFieldImageFile = self.xsDataInputSPD.getFlatFieldImageFile(
).getPath().getValue()
if os.path.isfile(pathToFlatFieldImageFile):
self.dictGeometry[
"FlatFieldImageFile"] = pathToFlatFieldImageFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToFlatFieldImageFile)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getSpatialDistortionFile() is not None:
pathToSpatialDistortionFile = self.xsDataInputSPD.getSpatialDistortionFile(
).getPath().getValue()
if os.path.isfile(pathToSpatialDistortionFile):
self.dictGeometry[
"SpatialDistortionFile"] = pathToSpatialDistortionFile
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToSpatialDistortionFile)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getAngleOfTilt() is not None:
if self.xsDataInputSPD.getAngleOfTilt().getUnit() is not None:
self.dictGeometry["AngleOfTilt"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getAngleOfTilt(), "deg")
else: #Fall-back by default to deg
self.WARNING(
"You did not specify the AngleOfTilt unit ... I Guess it is deg"
)
self.dictGeometry[
"AngleOfTilt"] = self.xsDataInputSPD.getAngleOfTilt(
).getValue()
else:
self.dictGeometry["AngleOfTilt"] = 0
if self.xsDataInputSPD.getTiltRotation() is not None:
if self.xsDataInputSPD.getTiltRotation().getUnit() is not None:
self.dictGeometry["TiltRotation"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getTiltRotation(), "deg")
else: #Fall-back by default to deg
self.WARNING(
"You did not specify the TiltRotation unit ... I Guess it is deg"
)
self.dictGeometry[
"TiltRotation"] = self.xsDataInputSPD.getTiltRotation(
).getValue()
else:
self.dictGeometry["TiltRotation"] = 0
if self.xsDataInputSPD.getBeamCentreInPixelsX() is not None:
self.dictGeometry[
"BeamCenterX"] = self.xsDataInputSPD.getBeamCentreInPixelsX(
).getValue()
if self.xsDataInputSPD.getBeamCentreInPixelsY() is not None:
self.dictGeometry[
"BeamCenterY"] = self.xsDataInputSPD.getBeamCentreInPixelsY(
).getValue()
if self.xsDataInputSPD.getBufferSizeX() is not None:
self.dictGeometry[
"BufferSizeX"] = self.xsDataInputSPD.getBufferSizeX().getValue(
)
if self.xsDataInputSPD.getBufferSizeY() is not None:
self.dictGeometry[
"BufferSizeY"] = self.xsDataInputSPD.getBufferSizeY().getValue(
)
if self.xsDataInputSPD.getDistortionFileX() is not None:
pathToDistortionFileX = self.xsDataInputSPD.getDistortionFileX(
).getPath().getValue()
if os.path.isfile(pathToDistortionFileX):
self.dictGeometry["DistortionFileX"] = pathToDistortionFileX
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDistortionFileX)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getDistortionFileY() is not None:
pathToDistortionFileY = self.xsDataInputSPD.getDistortionFileY(
).getPath().getValue()
if os.path.isfile(pathToDistortionFileY):
self.dictGeometry["DistortionFileY"] = pathToDistortionFileY
else:
edStringErrorMessage = EDMessage.ERROR_CANNOT_READ_FILE_02 % (
self.getPluginName() + ".preProcess",
pathToDistortionFileY)
self.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
if self.xsDataInputSPD.getPixelSizeX() is not None:
self.dictGeometry["PixelSizeX"] = EDUtilsUnit.getSIValue(
self.xsDataInputSPD.getPixelSizeX())
if self.xsDataInputSPD.getPixelSizeY() is not None:
self.dictGeometry["PixelSizeY"] = EDUtilsUnit.getSIValue(
self.xsDataInputSPD.getPixelSizeY())
if self.xsDataInputSPD.getSampleToDetectorDistance() is not None:
self.dictGeometry[
"SampleToDetectorDistance"] = EDUtilsUnit.getSIValue(
self.xsDataInputSPD.getSampleToDetectorDistance())
if self.xsDataInputSPD.getWavelength() is not None:
if self.xsDataInputSPD.getWavelength().getUnit() is not None:
self.dictGeometry["Wavelength"] = EDUtilsUnit.getSIValue(
self.xsDataInputSPD.getWavelength())
else: #Fall-back to Angsrom
self.WARNING(
"You did not specify the wavelength unit ... I Guess it is Angstrom"
)
self.dictGeometry[
"Wavelength"] = self.xsDataInputSPD.getWavelength(
).getValue() * 1e-10
if self.xsDataInputSPD.getOutputFileType() is not None:
self.dictGeometry[
"OutputFileType"] = self.xsDataInputSPD.getOutputFileType(
).getValue()
if not self.dictGeometry["OutputFileType"].startswith("."):
self.dictGeometry["OutputFileType"] = "." + self.dictGeometry[
"OutputFileType"]
else:
self.dictGeometry["OutputFileType"] = ".edf"
if self.xsDataInputSPD.getOutputDir() is not None:
tmpdir = self.xsDataInputSPD.getOutputDir().getPath().getValue()
if os.path.isdir(tmpdir):
self.dictGeometry["OutputDir"] = tmpdir
if tmpdir != os.path.dirname(self.pathToInputFile):
self._bFireAndForget = True
else:
self.WARNING(
"The destination directory %s does not exist, using working directory instead %s"
% (tmpdir, self.getWorkingDirectory()))
self.dictGeometry["OutputDir"] = self.getWorkingDirectory()
else:
self.dictGeometry["OutputDir"] = os.path.dirname(
self.pathToInputFile)
if self.dictGeometry["OutputDir"] == os.path.dirname(self.pathToInputFile) and \
not (self.pathToInputFile.endswith(self.dictGeometry["OutputFileType"])) and \
not (self.dictGeometry["OutputFileType"].lower() in [".h5", ".chi", ".nx", ".nexus", ".cif"]) :
self.bFireAndForget = True
def preProcess(self, _edObject=None):
"""
Preprocess: check the input parameters and unpack them
"""
EDPluginExec.preProcess(self)
EDVerbose.DEBUG("EDPluginExportAsciiPowderv1_0.preProcess")
if self.getDataInput().getEdfFile() is not None:
self.inputFilename = self.getDataInput().getEdfFile().getPath().getValue()
if not os.path.isfile(self.inputFilename):
EDVerbose.ERROR("The input file provided is not a valid file: %s" % self.inputFilename)
raise RuntimeError("Not a valid file %s" % self.inputFilename)
else:
self.readArrayFromFile(self.inputFilename)
elif self.getDataInput().getIntensities() is not None:
self.inputArray = EDUtilsArray.xsDataToArray(self.getDataInput().getIntensities())
else:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.preProcess: neither an input image, neither a data array given in input !"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if self.getDataInput().getDistance() is not None:
self.fDistance = EDUtilsUnit.getSIValue(self.getDataInput().getDistance())
if self.getDataInput().getPixelSize() is not None:
self.fPixelSize = EDUtilsUnit.getSIValue(self.getDataInput().getPixelSize())
if self.getDataInput().getOffset() is not None:
self.fRadOffset = self.getDataInput().getOffset().getValue()
if self.getDataInput().getOutputFormat() is not None:
self.strFormat = self.getDataInput().getOutputFormat().getValue().lower()
if self.getDataInput().getNumberOfBins() is not None:
self.iNbBins = self.getDataInput().getNumberOfBins().getValue()
if self.strFormat == "array":
self.outputFilename = None
else:
if self.getDataInput().getOutputFile() is None:
if "chi" in self.strFormat:
ext = ".chi"
elif "cif" in self.strFormat:
ext = ".cif"
elif "spr" in self.strFormat:
ext = ".spr"
else:
ext = ".powder"
self.outputFilename = os.path.join(self.getWorkingDirectory(), "output" + ext)
else:
self.outputFilename = self.getDataInput().getOutputFile().getPath().getValue()
if os.path.isdir(self.outputFilename):
if "chi" in self.strFormat:
ext = ".chi"
elif "cif" in self.strFormat:
ext = ".cif"
elif "spr" in self.strFormat:
ext = ".spr"
else:
ext = ".powder"
self.outputFilename = os.path.join(self.outputFilename,
os.path.splitext(os.path.basename(self.inputFilename))[0] + ext)
if (self.fPixelSize is None) or (self.fDistance is None):
strErrorMessage = "EDPluginExportAsciiPowderv1_0.preProcess: pixel size: %s; distance: %s Cannot be identified in %s !!!!" % (self.fPixelSize, self.fDistance, self.inputFilename)
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
def readArrayFromFile(self, _filename):
"""
Populate self.inputArray for a given filename and extracts as well
self.fPixelSize
self.fDistance
self.fRadOffset
self.wavelength ...
"""
image = openimage(_filename)
self.inputArray = image.data
self.dHeader = image.header
if "Offset_1" in self.dHeader:
offset, unit = self.dHeader["Offset_1"].split(None, 1)
if unit.lower() != "pixel":
EDVerbose.WARNING("I got a strange unit for offset: %s, I expected pixel." % self.dHeader["Offset_1"])
try:
self.fRadOffset = float(offset)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize this offset and convert it to float: %s" % self.dHeader["Offset_1"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if "Offset_2" in self.dHeader:
offset, unit = self.dHeader["Offset_2"].split(None, 1)
if unit.lower() != "pixel":
EDVerbose.WARNING("I got a strange unit for offset: %s, I expected pixel." % self.dHeader["Offset_2"])
try:
self.fAzimOffset = float(offset)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize this offset and convert it to float: %s" % self.dHeader["Offset_2"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
if "PSize_1" in self.dHeader:
psize, unit = self.dHeader["PSize_1"].split(None, 1)
try:
fPixelSize = float(psize)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the radial pixel size and convert it to float: %s" % self.dHeader["PSize_1"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.fPixelSize = EDUtilsUnit.getValueLength(fPixelSize, unit)
if "PSize_2" in self.dHeader:
psize, unit = self.dHeader["PSize_2"].split(None, 1)
try:
fPixelSize = float(psize)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the azimuthal pixel size and convert it to float: %s" % self.dHeader["PSize_2"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.fAzimSize = EDUtilsUnit.getValueAngle(fPixelSize, unit)
if ("SampleDistance" in self.dHeader):
distance, unit = self.dHeader["SampleDistance"].split(None, 1)
try:
fDistance = float(distance)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the Sample Distance is and convert it to float: %s" % self.dHeader["SampleDistance"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
self.fDistance = EDUtilsUnit.getValueLength(fDistance, unit)
if ("WaveLength" in self.dHeader):
wavelenth, unit = self.dHeader["WaveLength"].split(None, 1)
try:
fWavelength = float(wavelenth)
except ValueError:
strErrorMessage = "EDPluginExportAsciiPowderv1_0.process: Unable to recognize the wavelength is and convert it to float: %s" % self.dHeader["WaveLength"]
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise ValueError, strErrorMessage
self.fWavelength = EDUtilsUnit.getValueLength(fWavelength, unit)
if ("Dummy" in self.dHeader):
self.fDummy = float(self.dHeader.get("Dummy", 0))
if ("DDummy" in self.dHeader):
self.fDeltaDummy = float(self.dHeader.get("DDummy", 0.1))
def getInputParameter(self):
"""
Read all the input parameters and store them in instance variables called self.dictGeometry and self.pathToInputFile
"""
self.DEBUG("EDPluginSPDCakev1_5.getInputParameter")
EDPluginSPDCorrectv10.getInputParameter(self)
if self.xsDataInputSPD.getStartAzimuth() is not None:
if self.xsDataInputSPD.getStartAzimuth().getUnit() is not None:
self.dictGeometry["StartAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStartAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StartAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StartAzimuth"] = self.xsDataInputSPD.getStartAzimuth(
).getValue()
if self.xsDataInputSPD.getStopAzimuth() is not None:
if self.xsDataInputSPD.getStopAzimuth().getUnit() is not None:
self.dictGeometry["StopAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStopAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StopAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StopAzimuth"] = self.xsDataInputSPD.getStopAzimuth(
).getValue()
if self.xsDataInputSPD.getStepAzimuth() is not None:
if self.xsDataInputSPD.getStepAzimuth().getUnit() is not None:
self.dictGeometry["StepAzimuth"] = EDUtilsUnit.getValue(
self.xsDataInputSPD.getStepAzimuth(), "deg")
else:
self.WARNING(
"You did not specify the StepAzimuth Unit, Falling back to Deg (not Rad)"
)
self.dictGeometry[
"StepAzimuth"] = self.xsDataInputSPD.getStepAzimuth(
).getValue()
if self.xsDataInputSPD.getInnerRadius() is not None:
self.dictGeometry[
"InnerRadius"] = self.xsDataInputSPD.getInnerRadius().getValue(
)
if self.xsDataInputSPD.getOuterRadius() is not None:
self.dictGeometry[
"OuterRadius"] = self.xsDataInputSPD.getOuterRadius().getValue(
)
if self.xsDataInputSPD.getOutputDirCake() is not None:
self.dictGeometry[
"OutputDirCake"] = self.xsDataInputSPD.getOutputDirCake(
).getPath().getValue()
EDUtilsPath.createFolder(self.dictGeometry["OutputDirCake"])
if self.dictGeometry["OutputDirCake"] != self.dictGeometry[
"OutputDir"]:
self.setFireAndForget(False)
else:
self.dictGeometry["OutputDirCake"] = self.dictGeometry["OutputDir"]
if self.xsDataInputSPD.getMaskFile() is not None:
self.dictGeometry["MaskFile"] = self.xsDataInputSPD.getMaskFile(
).getPath().getValue()
if not os.path.isfile(self.dictGeometry["MaskFile"]):
self.ERROR("Mask file %s does not exist " %
self.dictGeometry["MaskFile"])
self.dictGeometry.pop("MaskFile")
if self.xsDataInputSPD.getIntensityScaleFactor() is not None:
self.dictGeometry[
"IntensityScaleFactor"] = self.xsDataInputSPD.getIntensityScaleFactor(
).getValue()
if self.xsDataInputSPD.getDeleteCorImg() is not None:
self.bDeleteCorImg = (
self.xsDataInputSPD.getDeleteCorImg().getValue()
in ["1", 1, "true", "True", True])
if self.bDeleteCorImg:
self.setFireAndForget(False)
if self.xsDataInputSPD.getCorrectTiltMask() is not None:
self.bCorrectTiltMask = bool(
self.xsDataInputSPD.getCorrectTiltMask().getValue())
def unitTestGetValueTime(self):
"""
Test conversion in Time
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetValueTime")
EDAssert.equal(60.0, EDUtilsUnit.getValue(EDUtilsUnit.toXSD(XSDataTime, "1 h"), "mn"), "Length Conversion h -> mn ")
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecNormalizeImagev1_1.preProcess")
sdi = self.getDataInput()
if sdi.getData() == []:
strError = "You should either provide at least ONE input filename or an array, you provided: %s" % sdi.marshal()
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
else:
for inputData in sdi.getData():
if inputData.exposureTime is None:
self.WARNING("You did not provide an exposure time for DATA... using default: 1")
self.listDataExposure.append(1.0)
else:
self.listDataExposure.append(EDUtilsUnit.getSIValue(inputData.exposureTime))
if inputData.path is not None:
strPath = inputData.path.value
if os.path.isfile(strPath):
self.listDataArray.append(fabio.open(strPath).data)
else:
strError = "The input file provided for DATA is not a valid file: %s" % strPath
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
elif inputData.array is not None:
self.listDataArray.append(EDUtilsArray.xsDataToArray(inputData.array))
else:
strError = "You should either provide an input filename or an array for DATA, you provided: %s" % inputData.marshal()
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
for inputFlat in sdi.getFlat():
if inputFlat.exposureTime is None:
self.WARNING("You did not provide an exposure time for FLAT... using default: 1")
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputFlat.exposureTime)
self.listFlatExposure.append(expTime)
if inputFlat.path is not None:
strPath = inputFlat.path.value
if os.path.isfile(strPath):
self.listFlatArray.append(fabio.open(strPath).data)
else:
strError = "The input file provided for FLAT is not a valid file: %s" % strPath
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
elif inputFlat.array is not None:
self.listFlatArray.append(EDUtilsArray.xsDataToArray(inputFlat.array))
else:
strError = "You should either provide an input filename or an array for FLAT, you provided: %s" % inputFlat.marshal()
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
with EDPluginExecNormalizeImagev1_1.semaphore:
for inputDark in sdi.getDark():
if inputDark.exposureTime is None:
self.WARNING("You did not provide an exposure time for Dark... using default: 1")
expTime = 1.0
else:
expTime = EDUtilsUnit.getSIValue(inputDark.exposureTime)
strMeanDarkKey = "/".join((self.getClassName(), "MeanDark%6.3f" % expTime))
if strMeanDarkKey not in EDShare:
self.listDarkExposure.append(expTime)
if inputDark.path is not None:
strPath = inputDark.path.value
if os.path.isfile(strPath):
self.listDarkArray.append(fabio.open(strPath).data)
else:
strError = "The input file provided for Dark is not a valid file: %s" % strPath
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
elif inputDark.array is not None:
self.listDarkArray.append(EDUtilsArray.xsDataToArray(inputDark.array))
elif inputDark.shared is not None:
self.listDarkArray.append(EDShare[inputDark.shared.value])
else:
strError = "You should either provide an input filename or an array for Dark, you provided: %s" % inputDark.marshal()
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
if sdi.output is not None:
if (sdi.output.path is not None):
self.strOutputFilename = sdi.output.path.value
elif (sdi.output.shared is not None):
self.strOutputShared = sdi.output.shared.value
# else export as array.
EDAssert.equal(len(self.listDataArray), len(self.listDataExposure), _strComment="number of data images / exposure times ")
EDAssert.equal(len(self.listFlatArray), len(self.listFlatExposure), _strComment="number of flat images / exposure times ")
EDAssert.equal(len(self.listDarkArray), len(self.listDarkExposure), _strComment="number of dark images / exposure times ")
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()
