def testCheckParameters(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(
self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.checkParameters()
def testSpatialDistortion(self):
strRefX = "spline-3-18x.edf"
strRefY = "spline-3-18y.edf"
self.loadTestImage([strRefX, strRefY])
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
########################################################################
# Enforce some values
########################################################################
edPluginSPD.dictGeometry["SpatialDistortionFile"] = os.path.join(self.getTestsDataImagesHome(), "frelon_spline_file_to_correct_SPD.spline")
edPluginSPD.dictGeometry["TiltRotation"] = 18
edPluginSPD.dictGeometry["AngleOfTilt"] = 3
spline = Spline()
spline.read(edPluginSPD.dictGeometry["SpatialDistortionFile"])
edPluginSPD.dictGeometry["PixelSizeX"], edPluginSPD.dictGeometry["PixelSizeY"] = spline.getPixelSize()
edPluginSPD.createDisplacementMatrix(spline)
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
refX = fabio.openimage.openimage(os.path.join(self.getTestsDataImagesHome(), strRefX)).data
obtX = fabio.openimage.openimage(os.path.join(edPluginSPD.getWorkingDirectory(), "frelon_spline_file_to_correct_SPD-tilted-x.edf")).data
refY = fabio.openimage.openimage(os.path.join(self.getTestsDataImagesHome(), strRefY)).data
obtY = fabio.openimage.openimage(os.path.join(edPluginSPD.getWorkingDirectory(), "frelon_spline_file_to_correct_SPD-tilted-y.edf")).data
# print edPluginSPD.dictGeometry
EDAssert.arraySimilar(obtX, refX , _fAbsMaxDelta=0.1, _strComment="X displacement Matrix is the same")
EDAssert.arraySimilar(obtY, refY , _fAbsMaxDelta=0.1, _strComment="Y displacement Matrix is the same")
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testPopulateXSDataInputSPDCake(self):
edPluginControlID11 = self.createPlugin()
xsDataInputSPDCake = edPluginControlID11.populateXSDataInputSPDCake(self.dictID11Reference)
strDataPath = self.getPluginTestsDataHome()
strReferenceFile = "XSDataInputSPDCake_fromDict.xml"
strPath = os.path.join(strDataPath, strReferenceFile)
xsDataInputSPDCakeReference = XSDataInputSPDCake.parseString(self.readAndParseFile(strPath))
xsDataInputSPDCakeReference.setDeleteCorImg(XSDataBoolean(not (EDVerbose.isVerboseDebug())))
EDAssert.equal(xsDataInputSPDCakeReference.marshal(), xsDataInputSPDCake.marshal())
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(
self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
if EDVerbose.isVerboseDebug():
edPluginSPD.cleanDispMat(edPluginSPD.getWorkingDirectory())
else:
edPluginSPD.cleanDispMat()
def testPopulateXSDataInputSPDCake(self):
edPluginControlID11 = self.createPlugin()
xsDataInputSPDCake = edPluginControlID11.populateXSDataInputSPDCake(
self.dictID11Reference)
strDataPath = self.getPluginTestsDataHome()
strReferenceFile = "XSDataInputSPDCake_fromDict.xml"
strPath = os.path.join(strDataPath, strReferenceFile)
xsDataInputSPDCakeReference = XSDataInputSPDCake.parseString(
self.readAndParseFile(strPath))
xsDataInputSPDCakeReference.setDeleteCorImg(
XSDataBoolean(not (EDVerbose.isVerboseDebug())))
EDAssert.equal(xsDataInputSPDCakeReference.marshal(),
xsDataInputSPDCake.marshal())
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(
self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile(
).getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(
strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[
strPathToParameterFile] = (
self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(
self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(
XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) *
int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(
self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" %
strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n%s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#"do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(
self.strReferenceInputFileName, EDUtilsPath.getDictOfPaths())
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n%s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#"do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0"""
#do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf cor_ext=.cor wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0"
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def testGenerateSPDCommand(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.configure()
edPluginSPD.getInputParameter()
#edPluginSPD.preProcess()
edPluginSPD.generateSPDCommand()
EDVerbose.screen("SPD configuration:\n %s" % edPluginSPD.getSPDConfig())
if EDVerbose.isVerboseDebug():
expected = """off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=2 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
else:
expected = """off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_distortion=0 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
# """do_distortion=2 off_1=0 off_2=0 verbose=0 src_ext=.edf wvl=1.000000e-10 cen_1=1.050000e+03 cen_2=1.000000e+03 dis=1.000000e-01 pix_1=4.722440e-05 pix_2=4.683150e-05 do_dark=0 cor_ext=.cor azim_int=1 azim_pass=0 azim_ext=.cor azim_r_num=1489"""
EDAssert.equal(edPluginSPD.getSPDConfig(), expected)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlID11v1_0.preProcess")
# Read the parameter file
if self.getDataInput().getCorrectMask() is not None:
self.bCorrectMask = bool(self.getDataInput().getCorrectMask().getValue())
strPathToParameterFile = self.getDataInput().getParameterFile().getPath().getValue()
if os.path.exists(strPathToParameterFile):
EDPluginControlID11v1_0.__semaphore.acquire()
if strPathToParameterFile in EDPluginControlID11v1_0.__dictParamID11XSD:
self.__dictID11, strInputSPDCake = EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile]
self.__xsDataInputSPDCake = XSDataInputSPDCake.parseString(strInputSPDCake)
else:
self.parseParameterFiles(strPathToParameterFile)
self.__xsDataInputSPDCake = self.populateXSDataInputSPDCake()
EDPluginControlID11v1_0.__dictParamID11XSD[strPathToParameterFile] = (self.__dictID11, self.__xsDataInputSPDCake.marshal())
EDPluginControlID11v1_0.__semaphore.release()
# Load the execution plugin
self.synchronizeOn()
self.__edPluginWaitMultipleFile = self.loadPlugin(self.__strControlledPluginWait)
self.synchronizeOff()
# self.__edPluginEDF = self.loadPlugin(self.__strControlledPluginEDF)
# Paths to the data files
self.__xsDataInputWaitMultipleFile = XSDataInputWaitMultiFile()
for xsDataFile in self.getDataInput().getDataFile():
self.__xsDataInputWaitMultipleFile.addExpectedFile(xsDataFile)
# we are expecting unsigned int
self.__xsDataInputWaitMultipleFile.setExpectedSize(XSDataInteger(512 + 2 * int(self.__dictID11["DIM1_DATA"]) * int(self.__dictID11["DIM2_DATA"])))
self.__edPluginWaitMultipleFile.setDataInput(self.__xsDataInputWaitMultipleFile)
else:
self.ERROR("Path to parameter file does not exist: %s" % strPathToParameterFile)
self.setFailure()
xsdOutputDir = self.getDataInput().getOutputdir()
if xsdOutputDir is not None:
self.__xsDataInputSPDCake.setOutputDir(xsdOutputDir)
self.__dictID11["output_dir"] = xsdOutputDir.getPath().getValue()
def populateXSDataInputSPDCake(dictID11):
xsDataInputSPDCake = XSDataInputSPDCake()
# Angle of tilt
xsDataInputSPDCake.setAngleOfTilt(
XSDataAngle(float(dictID11["ANGLE OF TILT"])))
# Dark current
if dictID11["DARK CURRENT"] == "YES":
xsDataInputSPDCake.setDarkCurrentImageFile(
XSDataFile(XSDataString(dictID11["DC FILE"])))
#xsDataFile = XSDataFile()
#xsDataFile.setPath(XSDataString(dictID11["DC FILE "]))
#xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
if dictID11["FLAT-FIELD"] == "YES":
xsDataInputSPDCake.setFlatFieldImageFile(
XSDataFile(XSDataString(dictID11["FF FILE"])))
if dictID11["FF SCALE"] == "NO":
xsDataInputSPDCake.setFlatFieldImageFile(
XSDataFile(XSDataString(dictID11["FF MULTIPLIER"])))
if dictID11["SPATIAL DIS."] == "YES":
xsDataInputSPDCake.setSpatialDistortionFile(
XSDataFile(XSDataString(dictID11["SD FILE"])))
xsDataInputSPDCake.setStartAzimuth(
XSDataAngle(float(dictID11["START AZIMUTH"])))
xsDataInputSPDCake.setStopAzimuth(
XSDataAngle(float(dictID11["END AZIMUTH"])))
xsDataInputSPDCake.setInnerRadius(
XSDataDouble(float(dictID11["INNER RADIUS"])))
xsDataInputSPDCake.setOuterRadius(
XSDataDouble(float(dictID11["OUTER RADIUS"])))
xsDataInputSPDCake.setBufferSizeX(
XSDataInteger(int(dictID11["X-PIXEL SIZE"])))
xsDataInputSPDCake.setBufferSizeY(
XSDataInteger(int(dictID11["Y-PIXEL SIZE"])))
xsDataInputSPDCake.setSampleToDetectorDistance(
XSDataLength(float(dictID11["DISTANCE"])))
xsDataInputSPDCake.setWavelength(
XSDataLength(float(dictID11["WAVELENGTH"])))
xsDataInputSPDCake.setBeamCentreInPixelsX(
XSDataDouble(float(dictID11["X-BEAM CENTRE"])))
xsDataInputSPDCake.setBeamCentreInPixelsY(
XSDataDouble(float(dictID11["Y-BEAM CENTRE"])))
xsDataInputSPDCake.setTiltRotation(
XSDataAngle(float(dictID11["TILT ROTATION"])))
xsDataInputSPDCake.setOutputFileType(
XSDataFile(XSDataString(dictID11["saving_format"])))
xsDataInputSPDCake.setOutputFileType(
XSDataFile(XSDataString(dictID11["output_dir"])))
# TODO : some parameters remain not inserted in this file because not in the datamodel
print xsDataInputSPDCake.marshal()
def testKillAllWorkers(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.killAllWorkers()
def testCleanDispMat(self):
edPluginSPD = self.createPlugin()
edStringXMLInput = EDUtilsTest.readAndParseFile(self.m_edStringReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(edStringXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.cleanDispMat()
def testKillAllWorkers(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.killAllWorkers()
def populateXSDataInputSPDCake(dictID11):
xsDataInputSPDCake = XSDataInputSPDCake()
# Angle of tilt
xsDataInputSPDCake.setAngleOfTilt(XSDataAngle(float(dictID11["ANGLE OF TILT"])))
# Dark current
if dictID11["DARK CURRENT"] == "YES":
xsDataInputSPDCake.setDarkCurrentImageFile(XSDataFile(XSDataString(dictID11["DC FILE"])))
#xsDataFile = XSDataFile()
#xsDataFile.setPath(XSDataString(dictID11["DC FILE "]))
#xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
if dictID11["FLAT-FIELD"] == "YES":
xsDataInputSPDCake.setFlatFieldImageFile(XSDataFile(XSDataString(dictID11["FF FILE"])))
if dictID11["FF SCALE"] == "NO":
xsDataInputSPDCake.setFlatFieldImageFile(XSDataFile(XSDataString(dictID11["FF MULTIPLIER"])))
if dictID11["SPATIAL DIS."] == "YES":
xsDataInputSPDCake.setSpatialDistortionFile(XSDataFile(XSDataString(dictID11["SD FILE"])))
xsDataInputSPDCake.setStartAzimuth(XSDataAngle(float(dictID11["START AZIMUTH"])))
xsDataInputSPDCake.setStopAzimuth(XSDataAngle(float(dictID11["END AZIMUTH"])))
xsDataInputSPDCake.setInnerRadius(XSDataDouble(float(dictID11["INNER RADIUS"])))
xsDataInputSPDCake.setOuterRadius(XSDataDouble(float(dictID11["OUTER RADIUS"])))
xsDataInputSPDCake.setBufferSizeX(XSDataInteger(int(dictID11["X-PIXEL SIZE"])))
xsDataInputSPDCake.setBufferSizeY(XSDataInteger(int(dictID11["Y-PIXEL SIZE"])))
xsDataInputSPDCake.setSampleToDetectorDistance(XSDataLength(float(dictID11["DISTANCE"])))
xsDataInputSPDCake.setWavelength(XSDataLength(float(dictID11["WAVELENGTH"])))
xsDataInputSPDCake.setBeamCentreInPixelsX(XSDataDouble(float(dictID11["X-BEAM CENTRE"])))
xsDataInputSPDCake.setBeamCentreInPixelsY(XSDataDouble(float(dictID11["Y-BEAM CENTRE"])))
xsDataInputSPDCake.setTiltRotation(XSDataAngle(float(dictID11["TILT ROTATION"])))
xsDataInputSPDCake.setOutputFileType(XSDataFile(XSDataString(dictID11["saving_format"])))
xsDataInputSPDCake.setOutputFileType(XSDataFile(XSDataString(dictID11["output_dir"])))
# TODO : some parameters remain not inserted in this file because not in the datamodel
print xsDataInputSPDCake.marshal()
def testCheckParameters(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsFile.readFileAndParseVariables(self.strReferenceInputFileName, {"${EDNA_TESTIMAGES}":"toto"})
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.checkParameters()
def testCheckParameters(self):
edPluginSPD = self.createPlugin()
strXMLInput = EDUtilsTest.readAndParseFile(self.strReferenceInputFileName)
xsDataInputSPDCake = XSDataInputSPDCake.parseString(strXMLInput)
edPluginSPD.setDataInput(xsDataInputSPDCake)
edPluginSPD.checkParameters()
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(
self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(
self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT"
in self.__dictID11) and (self.__dictID11["DARK CURRENT"]
== "YES"):
if ("DC FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"]
== "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning(
"Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"]
== "YES"):
if ("MASK FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"]
== "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning(
"Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !"
% (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(
XSDataDouble(1 / value))
else:
self.warning(
"Asked for FF SCALE correction but no FF MULTIPLIER provided"
)
if ("SPATIAL DIS."
in self.__dictID11) and (self.__dictID11["SPATIAL DIS."]
== "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else:
self.warning(
"Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file"
)
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(
self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue(
(float(self.__dictID11["END AZIMUTH"]) -
float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(
XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT" in self.__dictID11) and (self.__dictID11["DARK CURRENT"] == "YES") :
if ("DC FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"] == "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning("Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"] == "YES") :
if ("MASK FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"] == "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning("Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !" % (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(XSDataDouble(1 / value))
else:
self.warning("Asked for FF SCALE correction but no FF MULTIPLIER provided")
if ("SPATIAL DIS." in self.__dictID11) and (self.__dictID11["SPATIAL DIS."] == "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else :
self.warning("Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file")
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue((float(self.__dictID11["END AZIMUTH"]) - float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def 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
