コード例 #1
0
    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()
コード例 #2
0
    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()
コード例 #3
0
    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()