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 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 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()