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 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 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()
class EDPluginControlDiffractionCTv1_0(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by Fit2D for example and ....
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.m_strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.m_edPluginReadHeader = None
self.m_strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_0"
self.m_edPluginPowderIntegration = None
self.m_xsDataDiffractionCTInstrument = None
self.m_xsDataDiffractionCTImage = None
self.m_xsDataFileInputImage = None
self.m_edPluginControlledPluginWriteSinogram = None
self.m_strControlledPluginWriteSinogram = "EDPluginDCTWriteSinogramv1_0"
self.m_xsDataFileInputPowderDiffraction = None
self.m_xsDataResultDiffractionCT = None
self.m_edPluginWriteSinogram = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(),
"Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(),
"No path to input image")
self.checkMandatoryParameters(
self.getDataInput().getDestinationDirectory(),
"No path to destination directory")
self.checkMandatoryParameters(
self.getDataInput().getSinogramFileNamePrefix(),
"No sinogram prefix given")
self.checkMandatoryParameters(
self.getDataInput().getPowderDiffractionSubdirectory(),
"No subdirectory prefix for powder diffraction patterns")
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 process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.process")
self.m_edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
self.m_edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
self.m_edPluginPowderIntegration.connectSUCCESS(
self.doSuccessPowderIntegration)
self.m_edPluginPowderIntegration.connectFAILURE(
self.doFailurePowderIntegration)
self.m_edPluginWriteSinogram.connectSUCCESS(
self.doSuccessWriteSinogram)
self.m_edPluginWriteSinogram.connectFAILURE(
self.doFailureWriteSinogram)
self.m_edPluginReadHeader.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.postProcess")
self.setDataOutput(self.m_xsDataResultDiffractionCT)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput(
).getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if (strKey == "_diffrn_radiation_wavelength"):
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(
XSDataWavelength(float(strValue)))
elif (strKey == "_pd_instr_dist_spec/detc"):
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(
XSDataLength(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_max"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_min"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_meas_2theta_range_inc"):
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_synchrotron_photon-flux"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(
XSDataFlux(float(strValue)))
elif (strKey == "_synchrotron_ring-intensity"):
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(
XSDataDouble(float(strValue)))
elif (strKey == "_tomo_scan_ampl"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_scan_type"):
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(
XSDataString(strValue))
elif (strKey == "_tomo_spec_displ_rotation"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_rotation_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(
XSDataAngle(float(strValue)))
elif (strKey == "_tomo_spec_displ_x"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_x_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_inc"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_max"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(
XSDataLength(float(strValue)))
elif (strKey == "_tomo_spec_displ_z_min"):
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(
XSDataLength(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_angle"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(
XSDataAngle(float(strValue)))
elif (strKey == "_pd_instr_special_details_tilt_rotation"):
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(
XSDataAngle(float(strValue)))
elif (strKey == "_array_element_size[1]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_1(
XSDataLength(float(strValue)))
elif (strKey == "_array_element_size[2]"):
self.m_xsDataDiffractionCTImage.set_array_element_size_2(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[1]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(
XSDataLength(float(strValue)))
elif (strKey == "_diffrn_detector_element.center[2]"):
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(
XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif (strKey == "_file_correction_image_dark-current"):
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(
xsDataFileDark)
elif (strKey == "_file_correction_image_flat-field"):
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(
xsDataFileFlat)
elif (strKey == "_file_correction_image-mask"):
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(
xsDataFileMask)
elif (strKey == "_file_correction_spline_spatial-distortion"):
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(
xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(
self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(
self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(
xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
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 doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.m_edPluginWriteSinogram.getDataOutput(
)
if (xsDataResultWriteSinogram is not None):
self.m_xsDataResultDiffractionCT.setSinogramFile(
xsDataResultWriteSinogram.getSinogramFile())
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG(
"*** EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
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()
class EDPluginControlDiffractionCTv1_0(EDPluginControl):
"""
This is the EDNA control plug-in for diffraction contrast tomography.
It is intented to run 2D integration provided by Fit2D for example and ....
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputDiffractionCT)
self.m_strControlledPluginReadHeader = "EDPluginControlDCTReadHeaderv1_0"
self.m_edPluginReadHeader = None
self.m_strControlledPluginPowderIntegration = "EDPluginControlDCTPowderIntegrationv1_0"
self.m_edPluginPowderIntegration = None
self.m_xsDataDiffractionCTInstrument = None
self.m_xsDataDiffractionCTImage = None
self.m_xsDataFileInputImage = None
self.m_edPluginControlledPluginWriteSinogram = None
self.m_strControlledPluginWriteSinogram = "EDPluginDCTWriteSinogramv1_0"
self.m_xsDataFileInputPowderDiffraction = None
self.m_xsDataResultDiffractionCT = None
self.m_edPluginWriteSinogram = None
def checkParameters(self):
"""
Checks the mandatory parameters.
"""
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getImage(), "No path to input image")
self.checkMandatoryParameters(self.getDataInput().getDestinationDirectory(), "No path to destination directory")
self.checkMandatoryParameters(self.getDataInput().getSinogramFileNamePrefix(), "No sinogram prefix given")
self.checkMandatoryParameters(
self.getDataInput().getPowderDiffractionSubdirectory(),
"No subdirectory prefix for powder diffraction patterns",
)
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 process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.process")
self.m_edPluginReadHeader.connectSUCCESS(self.doSuccessReadHeader)
self.m_edPluginReadHeader.connectFAILURE(self.doFailureReadHeader)
self.m_edPluginPowderIntegration.connectSUCCESS(self.doSuccessPowderIntegration)
self.m_edPluginPowderIntegration.connectFAILURE(self.doFailurePowderIntegration)
self.m_edPluginWriteSinogram.connectSUCCESS(self.doSuccessWriteSinogram)
self.m_edPluginWriteSinogram.connectFAILURE(self.doFailureWriteSinogram)
self.m_edPluginReadHeader.executeSynchronous()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.postProcess")
self.setDataOutput(self.m_xsDataResultDiffractionCT)
def doSuccessReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessReadHeader")
# Translate dictionary to image and instrument objects
xsDataInputPowderIntegration = XSDataInputPowderIntegration()
self.m_xsDataDiffractionCTInstrument = XSDataDiffractionCTInstrument()
self.m_xsDataDiffractionCTImage = XSDataDiffractionCTImage()
xsDataDictionaryHeader = self.m_edPluginReadHeader.getDataOutput().getDictionary()
for xsDataKeyValuePair in xsDataDictionaryHeader.getKeyValuePair():
strKey = str(xsDataKeyValuePair.getKey().getValue())
strValue = str(xsDataKeyValuePair.getValue().getValue())
if strKey == "_diffrn_radiation_wavelength":
self.m_xsDataDiffractionCTInstrument.set_diffrn_radiation_wavelength(XSDataWavelength(float(strValue)))
elif strKey == "_pd_instr_dist_spec/detc":
self.m_xsDataDiffractionCTInstrument.set_pd_instr_dist_spec_detc(XSDataLength(float(strValue)))
elif strKey == "_pd_meas_2theta_range_max":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_max(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_min":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_min(XSDataAngle(float(strValue)))
elif strKey == "_pd_meas_2theta_range_inc":
self.m_xsDataDiffractionCTInstrument.set_pd_meas_2theta_range_inc(XSDataAngle(float(strValue)))
elif strKey == "_synchrotron_photon-flux":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_photon_flux(XSDataFlux(float(strValue)))
elif strKey == "_synchrotron_ring-intensity":
self.m_xsDataDiffractionCTInstrument.set_synchrotron_ring_intensity(XSDataDouble(float(strValue)))
elif strKey == "_tomo_scan_ampl":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_ampl(XSDataAngle(float(strValue)))
elif strKey == "_tomo_scan_type":
self.m_xsDataDiffractionCTInstrument.set_tomo_scan_type(XSDataString(strValue))
elif strKey == "_tomo_spec_displ_rotation":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_rotation_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_rotation_inc(XSDataAngle(float(strValue)))
elif strKey == "_tomo_spec_displ_x":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_x_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_x_min(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_inc":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_inc(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_max":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_max(XSDataLength(float(strValue)))
elif strKey == "_tomo_spec_displ_z_min":
self.m_xsDataDiffractionCTInstrument.set_tomo_spec_displ_z_min(XSDataLength(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_angle":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_angle(XSDataAngle(float(strValue)))
elif strKey == "_pd_instr_special_details_tilt_rotation":
self.m_xsDataDiffractionCTImage.set_pd_instr_special_details_tilt_rotation(XSDataAngle(float(strValue)))
elif strKey == "_array_element_size[1]":
self.m_xsDataDiffractionCTImage.set_array_element_size_1(XSDataLength(float(strValue)))
elif strKey == "_array_element_size[2]":
self.m_xsDataDiffractionCTImage.set_array_element_size_2(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[1]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_1(XSDataLength(float(strValue)))
elif strKey == "_diffrn_detector_element.center[2]":
self.m_xsDataDiffractionCTImage.set_diffrn_detector_element_center_2(XSDataLength(float(strValue)))
## Here the tricky case of lists ....
# elif strKey.startswith("_pd_sum_2theta_range_max"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_max()[pyintIndex] = XSDataAngle(float(strValue))
# elif strKey.startswith("_pd_sum_2theta_range_min"):
# if strKey.find("[")>0:
# pyintIndex = int(strKey.split("[")[1].split("]")[0]) - 1 #gets the int that is between []
# else:
# pyintIndex = 0
# while len(self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()) < pyintIndex + 1:
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min().append(None)
# self.m_xsDataDiffractionCTInstrument.get_pd_sum_2theta_range_min()[pyintIndex] = XSDataAngle(float(strValue))
##end Seems OK 20091023
elif strKey == "_file_correction_image_dark-current":
xsDataFileDark = XSDataFile()
xsDataFileDark.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_dark_current(xsDataFileDark)
elif strKey == "_file_correction_image_flat-field":
xsDataFileFlat = XSDataFile()
xsDataFileFlat.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_flat_field(xsDataFileFlat)
elif strKey == "_file_correction_image-mask":
xsDataFileMask = XSDataFile()
xsDataFileMask.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_image_mask(xsDataFileMask)
elif strKey == "_file_correction_spline_spatial-distortion":
xsDataFileSpatialDist = XSDataFile()
xsDataFileSpatialDist.setPath(XSDataString(strValue))
self.m_xsDataDiffractionCTImage.set_file_correction_spline_spatial_distortion(xsDataFileSpatialDist)
xsDataInputPowderIntegration.setImageParameters(self.m_xsDataDiffractionCTImage)
xsDataInputPowderIntegration.setInstrumentParameters(self.m_xsDataDiffractionCTInstrument)
xsDataInputPowderIntegration.setImageFile(self.m_xsDataFileInputImage)
self.m_edPluginPowderIntegration.setDataInput(xsDataInputPowderIntegration)
self.m_edPluginPowderIntegration.executeSynchronous()
def doFailureReadHeader(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureReadHeader")
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 doFailurePowderIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailurePowderIntegration")
def doSuccessWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doSuccessWriteSinogram")
xsDataResultWriteSinogram = self.m_edPluginWriteSinogram.getDataOutput()
if xsDataResultWriteSinogram is not None:
self.m_xsDataResultDiffractionCT.setSinogramFile(xsDataResultWriteSinogram.getSinogramFile())
def doFailureWriteSinogram(self, _edPlugin=None):
EDVerbose.DEBUG("*** EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlDiffractionCTv1_0.doFailureWriteSinogram")
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()
