def testCheckParameters(self):
xsDataFileIntegratedIntensities = XSDataFile()
xsDataFileIntegratedIntensities.setPath(XSDataString("/tmp/file.cif"))
xsDataFileSinogramDirectory = XSDataFile()
xsDataFileSinogramDirectory.setPath(XSDataString("/tmp"))
xsDataString = XSDataString("FakeExample")
xsDataInput = XSDataInputWriteSinogram()
xsDataInput.setIntegratedIntensities(xsDataFileIntegratedIntensities)
xsDataInput.setSinogramDirectory(xsDataFileSinogramDirectory)
xsDataInput.setSinogramFileNamePrefix(xsDataString)
edPluginExecDCTWriteSinogram = self.createPlugin()
edPluginExecDCTWriteSinogram.setDataInput(xsDataInput)
edPluginExecDCTWriteSinogram.checkParameters()
def testCheckParameters(self):
EDVerbose.DEBUG(
"EDTestCasePluginUnitControlDiffractionCTv1_0.testCheckParameters")
xsDataInput = XSDataInputDiffractionCT()
xsDataImage = XSDataImage()
xsDataInput.setImage(xsDataImage)
xsDataFile = XSDataFile()
xsDataInput.setDestinationDirectory(xsDataFile)
xsDataInput.setSinogramFileNamePrefix(XSDataString("FakePrefix"))
xsDataInput.setPowderDiffractionSubdirectory(XSDataString("Powder"))
edPluginControlDCTPowderIntegration = self.createPlugin()
edPluginControlDCTPowderIntegration.setDataInput(xsDataInput)
edPluginControlDCTPowderIntegration.checkParameters()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.preProcess")
# Load the execution plugin
self.m_edPluginReadHeader = self.loadPlugin(
self.m_strControlledPluginReadHeader)
self.m_edPluginPowderIntegration = self.loadPlugin(
self.m_strControlledPluginPowderIntegration)
self.m_edPluginWriteSinogram = self.loadPlugin(
self.m_strControlledPluginWriteSinogram)
# Set the input data for the read header plugin
xsDataInputReadHeader = XSDataInputReadHeader()
xsdataStringPathToImage = self.getDataInput().getImage().getPath()
self.m_xsDataFileInputImage = XSDataFile()
self.m_xsDataFileInputImage.setPath(xsdataStringPathToImage)
xsDataInputReadHeader.setInputFile(self.m_xsDataFileInputImage)
self.m_edPluginReadHeader.setDataInput(xsDataInputReadHeader)
def doSuccessPowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doSuccessPowderIntegration")
self.m_xsDataResultDiffractionCT = XSDataResultDiffractionCT()
# Copy file to final destination and add path to result object
xsDataFileIntegratedIntensities = self.m_edPluginPowderIntegration.getDataOutput(
).getIntegratedIntensities()
EDVerbose.DEBUG("Path to cif: " +
xsDataFileIntegratedIntensities.getPath().getValue())
EDVerbose.DEBUG("%s" % xsDataFileIntegratedIntensities)
if (xsDataFileIntegratedIntensities is not None):
strOutputFilePath = xsDataFileIntegratedIntensities.getPath(
).getValue()
strDestinationDirectory = self.getDataInput(
).getDestinationDirectory().getPath().getValue()
strPowderDiffractionSubdirectory = self.getDataInput(
).getPowderDiffractionSubdirectory().getValue()
if not os.path.isdir(strDestinationDirectory):
os.mkdir(strDestinationDirectory)
if self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type(
).getValue().lower() in ["flat", "spiral"]:
# pyintLineNumber = int( abs( float( self.cif[ "_tomo_spec_displ_rotation" ] ) / float( self.cif[ "_tomo_spec_displ_rotation_inc" ] ) ) )
pyintLineNumber = int(
abs(self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_rotation().getValue()) /
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_rotation_inc().getValue())
elif self.m_xsDataDiffractionCTInstrument.get_tomo_scan_type(
).getValue().lower(
) == "mapping": #I agree mappings are not sinograms but the really looks like, no ?
# pyintLineNumber = int( abs( ( float( self.cif[ "_tomo_spec_displ_z" ]) - float ( self.cif [ "_tomo_spec_displ_z_min" ] ) ) / float( self.cif["_tomo_spec_displ_z_inc"] ) ) )
pyintLineNumber = int(
abs(self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z().getValue() -
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z_min().getValue()) /
self.m_xsDataDiffractionCTInstrument.
get_tomo_spec_displ_z_inc().getValue())
else:
pyintLineNumber = None
if pyintLineNumber is not None:
pystrDestinationSubDir = "%s%04i" % (
strPowderDiffractionSubdirectory, pyintLineNumber)
strDestinationDirectoryWithSub = os.path.join(
strDestinationDirectory, pystrDestinationSubDir)
strDestinationFilePath = os.path.join(
strDestinationDirectoryWithSub,
os.path.basename(strOutputFilePath))
if not os.path.isdir(
os.path.join(strDestinationDirectoryWithSub)):
os.mkdir(strDestinationDirectoryWithSub)
EDVerbose.DEBUG("Full path should be now: %s" %
strDestinationFilePath)
else:
EDVerbose.DEBUG(
"No modification of the output directory: I was not able to determine on which line of the sinogram I am."
)
strDestinationFilePath = os.path.abspath(
os.path.join(strDestinationDirectory,
EDUtilsFile.getBaseName(strOutputFilePath)))
EDUtilsFile.copyFile(strOutputFilePath, strDestinationFilePath)
xsDataFileDestination = XSDataFile()
xsDataFileDestination.setPath(XSDataString(strDestinationFilePath))
self.m_xsDataResultDiffractionCT.setIntegratedIntensities(
xsDataFileDestination)
xsDataPathSinogramDirectory = XSDataFile()
xsDataPathSinogramDirectory.setPath(
XSDataString(strDestinationDirectory))
xsDataInputWriteSinogram = XSDataInputWriteSinogram()
xsDataInputWriteSinogram.setSinogramDirectory(
xsDataPathSinogramDirectory)
xsDataInputWriteSinogram.setIntegratedIntensities(
xsDataFileDestination)
xsDataInputWriteSinogram.setSinogramFileNamePrefix(
self.getDataInput().getSinogramFileNamePrefix())
self.m_edPluginWriteSinogram.setDataInput(xsDataInputWriteSinogram)
self.m_edPluginWriteSinogram.executeSynchronous()
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput(
).getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if (strKey == "_diffrn_radiation_wavelength"):
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(
XSDataWavelength(float(strValue)))
elif (strKey == "_pd_instr_dist_spec/detc"):
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(
XSDataLength(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_max"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_min"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_inc"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_synchrotron_photon-flux"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(
XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(
XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_scan_type"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(
XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_rotation_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_x"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(
XSDataLength(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_angle"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_array_element_size[1]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_1(
XSDataLength(float(strValue)))
elif (strKey == "_array_element_size[2]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_2(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[1]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[2]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(
XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(
xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(
xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(
xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(
xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(
self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(
self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(
xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
