def runTest(self):
     # Load processed vanadium for normalisation (bank 1)
     van = LoadNexus(Filename="WISH19612_vana_bank1_SXProcessed.nxs")
     # Load raw data (bank 1)
     ws = load_data_and_normalise(
         "WISH00038237.raw")  # default so doesn't get overwrite van
     # normalise to vanadium
     RebinToWorkspace(WorkspaceToRebin=van,
                      WorkspaceToMatch=ws,
                      OutputWorkspace=van)
     Divide(LHSWorkspace=ws, RHSWorkspace=van, OutputWorkspace=ws)
     ReplaceSpecialValues(InputWorkspace=ws,
                          OutputWorkspace=ws,
                          NaNValue=0,
                          InfinityValue=0,
                          BigNumberThreshold=1e15,
                          SmallNumberThreshold=-1e15)
     # Convert to Diffraction MD and Lorentz Correction
     wsMD = ConvertToDiffractionMDWorkspace(InputWorkspace=ws,
                                            LorentzCorrection=True,
                                            OneEventPerBin=False)
     # BinMD to 2D object and convert to histo so can compare saved workspace
     wsMD_2Dcut = BinMD(InputWorkspace=wsMD,
                        AxisAligned=False,
                        BasisVector0='Q_lab_x,Angstrom^-1,1.0,0.0,0.0',
                        BasisVector1='Q_lab_y,Angstrom^-1,0.0,1.0,0.0',
                        BasisVector2='Q_lab_z,Angstrom^-1,0.0,0.0,1.0',
                        OutputExtents='0.2,0.8,-0.4,0.4,0.05,0.1',
                        OutputBins='50,50,1')
     ConvertMDHistoToMatrixWorkspace(InputWorkspace=wsMD_2Dcut,
                                     outputWorkspace="wsHisto_2Dcut")
Пример #2
0
 def _whole_inst_prefocus(input_workspace, vanadium_integration_ws,
                          full_calib) -> bool:
     """This is used to perform the operations done on the whole instrument workspace, before the chosen region of
     interest is focused using _run_focus
     :param input_workspace: Raw sample run to process prior to focussing over a region of interest
     :param vanadium_integration_ws: Integral of the supplied vanadium run
     :param full_calib: Full instrument calibration workspace (table ws output from PDCalibration)
     :return True if successful, False if aborted
     """
     if input_workspace.getRun().getProtonCharge() > 0:
         NormaliseByCurrent(InputWorkspace=input_workspace,
                            OutputWorkspace=input_workspace)
     else:
         logger.warning(
             f"Skipping focus of run {input_workspace.name()} because it has invalid proton charge."
         )
         return False
     input_workspace /= vanadium_integration_ws
     # replace nans created in sensitivity correction
     ReplaceSpecialValues(InputWorkspace=input_workspace,
                          OutputWorkspace=input_workspace,
                          NaNValue=0,
                          InfinityValue=0)
     ApplyDiffCal(InstrumentWorkspace=input_workspace,
                  CalibrationWorkspace=full_calib)
     ConvertUnits(InputWorkspace=input_workspace,
                  OutputWorkspace=input_workspace,
                  Target='dSpacing')
     return True
Пример #3
0
def divide_workspace(dividend_workspace, divisor_workspace):
    """
    Divides the specified dividend workspace by the specified divisor workspace.
    Replaces Infinity and NaNValues with 0.

    :param dividend_workspace: The workspace to be divided.
    :param divisor_workspace:  The workspace to divide by.
    :return:                   The dividend workspace / the divisor workspace.
    """
    dividend_ws, divisor_ws = rebin_to_smallest(dividend_workspace, divisor_workspace)
    divided_ws = Divide(LHSWorkspace=dividend_ws, RHSWorkspace=divisor_ws,
                        OutputWorkspace="divided", StoreInADS=False, EnableLogging=False)
    return ReplaceSpecialValues(InputWorkspace=divided_ws,
                                NaNValue=0.0, InfinityValue=0.0,
                                OutputWorkspace="removed_special",
                                StoreInADS=False, EnableLogging=False)
Пример #4
0
 def runTest(self):
     try:
         BASISPowderDiffraction(RunNumbers='74799',
                                FluxNormalizationType='Monitor',
                                OutputWorkspace='powder_Mon',
                                MaskFile='BASIS_Mask_default_diff.xml')
         BASISPowderDiffraction(RunNumbers='74799',
                                FluxNormalizationType='Proton Charge',
                                OutputWorkspace='powder_Pro',
                                MaskFile='BASIS_Mask_default_diff.xml')
         Divide(LHSWorkspace='powder_Pro',
                RHSWorkspace='powder_Mon',
                OutputWorkspace='powder_ratio')
         ReplaceSpecialValues(InputWorkspace='powder_ratio',
                              NANValue=1.0,
                              NANError=1.0,
                              OutputWorkspace='powder_ratio')
     finally:
         self.preptear()
def load_data_and_normalise(filename,
                            spectrumMin=1,
                            spectrumMax=19461,
                            outputWorkspace="sample"):
    """
    Function to load in raw data, crop and normalise
    :param filename: file path to .raw
    :param spectrumMin: min spec to load (default incl. all monitors)
    :param spectrumMax: max spec to load (default includes only bank 1)
    :param outputWorkspace: name of output workspace (can be specified to stop workspaces being overwritten)
    :return: normalised and cropped data with xunit wavelength (excl. monitors)
    """
    sample, mon = LoadRaw(Filename=filename,
                          SpectrumMin=spectrumMin,
                          SpectrumMax=spectrumMax,
                          LoadMonitors="Separate",
                          OutputWorkspace=outputWorkspace)
    for ws in [sample, mon]:
        CropWorkspace(InputWorkspace=ws,
                      OutputWorkspace=ws,
                      XMin=6000,
                      XMax=99000)
        NormaliseByCurrent(InputWorkspace=ws, OutputWorkspace=ws)
        ConvertUnits(InputWorkspace=ws,
                     OutputWorkspace=ws,
                     Target='Wavelength')
    NormaliseToMonitor(InputWorkspace=sample,
                       OutputWorkspace=sample,
                       MonitorWorkspaceIndex=3,
                       MonitorWorkspace=mon)
    ReplaceSpecialValues(InputWorkspace=sample,
                         OutputWorkspace=sample,
                         NaNValue=0,
                         InfinityValue=0)
    CropWorkspace(InputWorkspace=sample,
                  OutputWorkspace=sample,
                  XMin=0.8,
                  XMax=9.3)
    return sample
Пример #6
0
def _calculate_vanadium_processed_instrument(van_ws, full_calib_ws,
                                             integral_ws,
                                             run_no):  # -> Workspace
    """
    Calculate the processed whole-instrument workspace
    :param van_ws: Chosen vanadium run workspace
    :param full_calib_ws: Table workspace from the full instrument calibration (output from PDCalibration)
    :param integral_ws: Vanadium integral workspace
    :return: Whole instrument processed workspace
    """
    ws = NormaliseByCurrent(
        InputWorkspace=van_ws,
        OutputWorkspace=str(run_no) + "_" +
        PROCESSED_WORKSPACE_NAME)  # create new name ws here
    ApplyDiffCal(InstrumentWorkspace=ws, CalibrationWorkspace=full_calib_ws)
    ConvertUnits(InputWorkspace=ws, OutputWorkspace=ws, Target='dSpacing')
    # van sensitivity correction
    ws /= integral_ws
    ReplaceSpecialValues(InputWorkspace=ws,
                         OutputWorkspace=ws,
                         NaNValue=0,
                         InfinityValue=0)
    return ws
Пример #7
0
    def PyExec(self):
        # Retrieve all relevant notice

        in_Runs = self.getProperty("RunNumbers").value

        maskWSname = self._getMaskWSname()

        # either type of file-based calibration is stored in the same variable
        calib = self.getProperty("Calibration").value
        if calib == "Calibration File":
            cal_File = self.getProperty("CalibrationFilename").value
        elif calib == 'DetCal File':
            cal_File = self.getProperty('DetCalFilename').value
            cal_File = ','.join(cal_File)
        else:
            cal_File = None

        params = self.getProperty("Binning").value
        norm = self.getProperty("Normalization").value

        if norm == "From Processed Nexus":
            norm_File = self.getProperty("NormalizationFilename").value
            LoadNexusProcessed(Filename=norm_File, OutputWorkspace='normWS')
            normWS = 'normWS'
        elif norm == "From Workspace":
            normWS = str(self.getProperty("NormalizationWorkspace").value)
        else:
            normWS = None

        group_to_real = {
            'Banks': 'Group',
            'Modules': 'bank',
            '2_4 Grouping': '2_4Grouping'
        }
        group = self.getProperty('GroupDetectorsBy').value
        real_name = group_to_real.get(group, group)

        if not mtd.doesExist(group):
            if group == '2_4 Grouping':
                group = '2_4_Grouping'
            CreateGroupingWorkspace(InstrumentName='SNAP',
                                    GroupDetectorsBy=real_name,
                                    OutputWorkspace=group)

        Process_Mode = self.getProperty("ProcessingMode").value

        prefix = self.getProperty("OptionalPrefix").value

        # --------------------------- REDUCE DATA -----------------------------

        Tag = 'SNAP'
        for r in in_Runs:
            self.log().notice("processing run %s" % r)
            self.log().information(str(self.get_IPTS_Local(r)))
            if self.getProperty("LiveData").value:
                Tag = 'Live'
                LoadPreNexusLive(Instrument='SNAP', OutputWorkspace='WS')
            else:
                Load(Filename='SNAP' + str(r), OutputWorkspace='WS')
                NormaliseByCurrent(InputWorkspace='WS', OutputWorkspace='WS')

            CompressEvents(InputWorkspace='WS', OutputWorkspace='WS')
            CropWorkspace(InputWorkspace='WS',
                          OutputWorkspace='WS',
                          XMax=50000)
            RemovePromptPulse(InputWorkspace='WS',
                              OutputWorkspace='WS',
                              Width='1600',
                              Frequency='60.4')

            if maskWSname is not None:
                MaskDetectors(Workspace='WS', MaskedWorkspace=maskWSname)

            self._alignAndFocus(params, calib, cal_File, group)

            normWS = self._generateNormalization('WS_red', norm, normWS)
            WS_nor = None
            if normWS is not None:
                WS_nor = 'WS_nor'
                Divide(LHSWorkspace='WS_red',
                       RHSWorkspace=normWS,
                       OutputWorkspace='WS_nor')
                ReplaceSpecialValues(Inputworkspace='WS_nor',
                                     OutputWorkspace='WS_nor',
                                     NaNValue='0',
                                     NaNError='0',
                                     InfinityValue='0',
                                     InfinityError='0')

            new_Tag = Tag
            if len(prefix) > 0:
                new_Tag += '_' + prefix

            # Edit instrument geomety to make final workspace smaller on disk
            det_table = PreprocessDetectorsToMD(
                Inputworkspace='WS_red', OutputWorkspace='__SNAP_det_table')
            polar = np.degrees(det_table.column('TwoTheta'))
            azi = np.degrees(det_table.column('Azimuthal'))
            EditInstrumentGeometry(Workspace='WS_red',
                                   L2=det_table.column('L2'),
                                   Polar=polar,
                                   Azimuthal=azi)
            if WS_nor is not None:
                EditInstrumentGeometry(Workspace='WS_nor',
                                       L2=det_table.column('L2'),
                                       Polar=polar,
                                       Azimuthal=azi)
            mtd.remove('__SNAP_det_table')

            # Save requested formats
            basename = '%s_%s_%s' % (new_Tag, r, group)
            self._save(r, basename, norm)

            # temporary workspace no longer needed
            DeleteWorkspace(Workspace='WS')

            # rename everything as appropriate and determine output workspace name
            RenameWorkspace(Inputworkspace='WS_d',
                            OutputWorkspace='%s_%s_d' % (new_Tag, r))
            RenameWorkspace(Inputworkspace='WS_red',
                            OutputWorkspace=basename + '_red')
            if norm == 'None':
                outputWksp = basename + '_red'
            else:
                outputWksp = basename + '_nor'
                RenameWorkspace(Inputworkspace='WS_nor',
                                OutputWorkspace=basename + '_nor')
            if norm == "Extracted from Data":
                RenameWorkspace(Inputworkspace='peak_clip_WS',
                                OutputWorkspace='%s_%s_normalizer' %
                                (new_Tag, r))

            # delte some things in production
            if Process_Mode == "Production":
                DeleteWorkspace(Workspace='%s_%s_d' %
                                (new_Tag, r))  # was 'WS_d'

                if norm != "None":
                    DeleteWorkspace(Workspace=basename +
                                    '_red')  # was 'WS_red'

                if norm == "Extracted from Data":
                    DeleteWorkspace(Workspace='%s_%s_normalizer' %
                                    (new_Tag, r))  # was 'peak_clip_WS'

            propertyName = 'OutputWorkspace_' + str(outputWksp)
            self.declareProperty(
                WorkspaceProperty(propertyName, outputWksp, Direction.Output))
            self.setProperty(propertyName, outputWksp)
Пример #8
0
    def PyExec(self):
        in_Runs = self.getProperty("RunNumbers").value
        progress = Progress(self, 0., .25, 3)
        finalUnits = self.getPropertyValue("FinalUnits")
        self.chunkSize = self.getProperty('MaxChunkSize').value

        # default arguments for AlignAndFocusPowder
        self.alignAndFocusArgs = {'Tmin': 0,
                                  'TMax': 50000,
                                  'RemovePromptPulseWidth': 1600,
                                  'PreserveEvents': False,
                                  'Dspacing': True,  # binning parameters in d-space
                                  'Params': self.getProperty("Binning").value,
                                  }

        # workspace for loading metadata only to be used in LoadDiffCal and
        # CreateGroupingWorkspace
        metaWS = None

        # either type of file-based calibration is stored in the same variable
        calib = self.getProperty("Calibration").value
        detcalFile = None
        if calib == "Calibration File":
            metaWS = self._loadMetaWS(in_Runs[0])
            LoadDiffCal(Filename=self.getPropertyValue("CalibrationFilename"),
                        WorkspaceName='SNAP',
                        InputWorkspace=metaWS,
                        MakeGroupingWorkspace=False, MakeMaskWorkspace=False)
            self.alignAndFocusArgs['CalibrationWorkspace'] = 'SNAP_cal'
        elif calib == 'DetCal File':
            detcalFile = ','.join(self.getProperty('DetCalFilename').value)
        progress.report('loaded calibration')

        norm = self.getProperty("Normalization").value

        if norm == "From Processed Nexus":
            norm_File = self.getProperty("NormalizationFilename").value
            normalizationWS = 'normWS'
            LoadNexusProcessed(Filename=norm_File, OutputWorkspace=normalizationWS)
            progress.report('loaded normalization')
        elif norm == "From Workspace":
            normalizationWS = str(self.getProperty("NormalizationWorkspace").value)
            progress.report('')
        else:
            normalizationWS = None
            progress.report('')

        self.alignAndFocusArgs['GroupingWorkspace'] = self._generateGrouping(in_Runs[0], metaWS, progress)
        self.alignAndFocusArgs['MaskWorkspace'] = self._getMaskWSname(in_Runs[0], metaWS)  # can be empty string

        if metaWS is not None:
            DeleteWorkspace(Workspace=metaWS)

        Process_Mode = self.getProperty("ProcessingMode").value

        prefix = self.getProperty("OptionalPrefix").value

        Tag = 'SNAP'
        progStart = .25
        progDelta = (1.-progStart)/len(in_Runs)

        # --------------------------- PROCESS BACKGROUND ----------------------
        if not self.getProperty('Background').isDefault:
            progDelta = (1. - progStart) / (len(in_Runs) + 1)  # redefine to account for background

            background = 'SNAP_{}'.format(self.getProperty('Background').value)
            self.log().notice("processing run background {}".format(background))
            background, unfocussedBkgd = self._alignAndFocus(background,
                                                             background+'_bkgd_red',
                                                             detCalFilename=detcalFile,
                                                             withUnfocussed=(Process_Mode == 'Set-Up'),
                                                             progStart=progStart, progDelta=progDelta)
        else:
            background = None
            unfocussedBkgd = ''

        # --------------------------- REDUCE DATA -----------------------------

        for i, runnumber in enumerate(in_Runs):
            self.log().notice("processing run %s" % runnumber)

            # put together output names
            new_Tag = Tag
            if len(prefix) > 0:
                new_Tag = prefix + '_' + new_Tag
            basename = '%s_%s_%s' % (new_Tag, runnumber, self.alignAndFocusArgs['GroupingWorkspace'])
            self.log().warning('{}:{}:{}'.format(i, new_Tag, basename))
            redWS, unfocussedWksp = self._alignAndFocus('SNAP_{}'.format(runnumber),
                                                        basename + '_red',
                                                        detCalFilename=detcalFile,
                                                        withUnfocussed=(Process_Mode == 'Set-Up'),
                                                        progStart=progStart, progDelta=progDelta*.5)
            progStart += .5 * progDelta

            # subtract the background if it was supplied
            if background:
                self.log().information('subtracting {} from {}'.format(background, redWS))
                Minus(LHSWorkspace=redWS, RHSWorkspace=background, OutputWorkspace=redWS)
                # intentionally don't subtract the unfocussed workspace since it hasn't been normalized by counting time

            # the rest takes up .25 percent of the run processing
            progress = Progress(self, progStart, progStart+.25*progDelta, 2)

            # AlignAndFocusPowder leaves the data in time-of-flight
            ConvertUnits(InputWorkspace=redWS, OutputWorkspace=redWS, Target='dSpacing', EMode='Elastic')

            # Edit instrument geometry to make final workspace smaller on disk
            det_table = PreprocessDetectorsToMD(Inputworkspace=redWS,
                                                OutputWorkspace='__SNAP_det_table')
            polar = np.degrees(det_table.column('TwoTheta'))
            azi = np.degrees(det_table.column('Azimuthal'))
            EditInstrumentGeometry(Workspace=redWS, L2=det_table.column('L2'),
                                   Polar=polar, Azimuthal=azi)
            mtd.remove('__SNAP_det_table')
            progress.report('simplify geometry')

            # AlignAndFocus doesn't necessarily rebin the data correctly
            if Process_Mode == "Set-Up":
                Rebin(InputWorkspace=unfocussedWksp, Params=self.alignAndFocusArgs['Params'],
                      Outputworkspace=unfocussedWksp)
                if background:
                    Rebin(InputWorkspace=unfocussedBkgd, Params=self.alignAndFocusArgs['Params'],
                          Outputworkspace=unfocussedBkgd)
            # normalize the data as requested
            normalizationWS = self._generateNormalization(redWS, norm, normalizationWS)
            normalizedWS = None
            if normalizationWS is not None:
                normalizedWS = basename + '_nor'
                Divide(LHSWorkspace=redWS, RHSWorkspace=normalizationWS,
                       OutputWorkspace=normalizedWS)
                ReplaceSpecialValues(Inputworkspace=normalizedWS,
                                     OutputWorkspace=normalizedWS,
                                     NaNValue='0', NaNError='0',
                                     InfinityValue='0', InfinityError='0')
                progress.report('normalized')
            else:
                progress.report()

            # rename everything as appropriate and determine output workspace name
            if normalizedWS is None:
                outputWksp = redWS
            else:
                outputWksp = normalizedWS

                if norm == "Extracted from Data" and Process_Mode == "Production":
                        DeleteWorkspace(Workspace=redWS)
                        DeleteWorkspace(Workspace=normalizationWS)

            # Save requested formats - function checks that saving is requested
            self._save(runnumber, basename, outputWksp)

            # set workspace as an output so it gets history
            ConvertUnits(InputWorkspace=str(outputWksp), OutputWorkspace=str(outputWksp), Target=finalUnits,
                         EMode='Elastic')
            self._exportWorkspace('OutputWorkspace_' + str(outputWksp), outputWksp)

            # declare some things as extra outputs in set-up
            if Process_Mode != "Production":
                propprefix = 'OutputWorkspace_{:d}_'.format(i)
                propNames = [propprefix + it for it in ['d', 'norm', 'normalizer']]
                wkspNames = ['%s_%s_d' % (new_Tag, runnumber),
                             basename + '_red',
                             '%s_%s_normalizer' % (new_Tag, runnumber)]
                for (propName, wkspName) in zip(propNames, wkspNames):
                    self._exportWorkspace(propName, wkspName)

        if background:
            ConvertUnits(InputWorkspace=str(background), OutputWorkspace=str(background), Target=finalUnits,
                         EMode='Elastic')
            prefix = 'OutputWorkspace_{}'.format(len(in_Runs))
            propNames = [prefix + it for it in ['', '_d']]
            wkspNames = [background, unfocussedBkgd]
            for (propName, wkspName) in zip(propNames, wkspNames):
                self._exportWorkspace(propName, wkspName)
Пример #9
0
    def PyExec(self):
        in_Runs = self.getProperty("RunNumbers").value
        maskWSname = self._getMaskWSname()
        progress = Progress(self, 0., .25, 3)

        # default arguments for AlignAndFocusPowder
        alignAndFocusArgs = {
            'TMax': 50000,
            'RemovePromptPulseWidth': 1600,
            'PreserveEvents': False,
            'Dspacing': True,  # binning parameters in d-space
            'Params': self.getProperty("Binning").value
        }

        # workspace for loading metadata only to be used in LoadDiffCal and
        # CreateGroupingWorkspace
        metaWS = None

        # either type of file-based calibration is stored in the same variable
        calib = self.getProperty("Calibration").value
        detcalFile = None
        if calib == "Calibration File":
            metaWS = self._loadMetaWS(in_Runs[0])
            LoadDiffCal(Filename=self.getPropertyValue("CalibrationFilename"),
                        WorkspaceName='SNAP',
                        InputWorkspace=metaWS,
                        MakeGroupingWorkspace=False,
                        MakeMaskWorkspace=False)
            alignAndFocusArgs['CalibrationWorkspace'] = 'SNAP_cal'
        elif calib == 'DetCal File':
            detcalFile = ','.join(self.getProperty('DetCalFilename').value)
        progress.report('loaded calibration')

        norm = self.getProperty("Normalization").value

        if norm == "From Processed Nexus":
            norm_File = self.getProperty("NormalizationFilename").value
            normalizationWS = 'normWS'
            LoadNexusProcessed(Filename=norm_File,
                               OutputWorkspace=normalizationWS)
            progress.report('loaded normalization')
        elif norm == "From Workspace":
            normalizationWS = str(
                self.getProperty("NormalizationWorkspace").value)
            progress.report('')
        else:
            normalizationWS = None
            progress.report('')

        group = self._generateGrouping(in_Runs[0], metaWS, progress)

        if metaWS is not None:
            DeleteWorkspace(Workspace=metaWS)

        Process_Mode = self.getProperty("ProcessingMode").value

        prefix = self.getProperty("OptionalPrefix").value

        # --------------------------- REDUCE DATA -----------------------------

        Tag = 'SNAP'
        if self.getProperty("LiveData").value:
            Tag = 'Live'

        progStart = .25
        progDelta = (1. - progStart) / len(in_Runs)
        for i, runnumber in enumerate(in_Runs):
            self.log().notice("processing run %s" % runnumber)
            self.log().information(str(self.get_IPTS_Local(runnumber)))

            # put together output names
            new_Tag = Tag
            if len(prefix) > 0:
                new_Tag += '_' + prefix
            basename = '%s_%s_%s' % (new_Tag, runnumber, group)

            if self.getProperty("LiveData").value:
                raise RuntimeError('Live data is not currently supported')
            else:
                Load(Filename='SNAP' + str(runnumber),
                     OutputWorkspace=basename + '_red',
                     startProgress=progStart,
                     endProgress=progStart + .25 * progDelta)
                progStart += .25 * progDelta
            redWS = basename + '_red'

            # overwrite geometry with detcal files
            if calib == 'DetCal File':
                LoadIsawDetCal(InputWorkspace=redWS, Filename=detcalFile)

            # create unfocussed data if in set-up mode
            if Process_Mode == "Set-Up":
                unfocussedWksp = '{}_{}_d'.format(new_Tag, runnumber)
            else:
                unfocussedWksp = ''

            AlignAndFocusPowder(
                InputWorkspace=redWS,
                OutputWorkspace=redWS,
                MaskWorkspace=maskWSname,  # can be empty string
                GroupingWorkspace=group,
                UnfocussedWorkspace=unfocussedWksp,  # can be empty string
                startProgress=progStart,
                endProgress=progStart + .5 * progDelta,
                **alignAndFocusArgs)
            progStart += .5 * progDelta

            # the rest takes up .25 percent of the run processing
            progress = Progress(self, progStart, progStart + .25 * progDelta,
                                2)

            # AlignAndFocusPowder leaves the data in time-of-flight
            ConvertUnits(InputWorkspace=redWS,
                         OutputWorkspace=redWS,
                         Target='dSpacing',
                         EMode='Elastic')

            # Edit instrument geometry to make final workspace smaller on disk
            det_table = PreprocessDetectorsToMD(
                Inputworkspace=redWS, OutputWorkspace='__SNAP_det_table')
            polar = np.degrees(det_table.column('TwoTheta'))
            azi = np.degrees(det_table.column('Azimuthal'))
            EditInstrumentGeometry(Workspace=redWS,
                                   L2=det_table.column('L2'),
                                   Polar=polar,
                                   Azimuthal=azi)
            mtd.remove('__SNAP_det_table')
            progress.report('simplify geometry')

            # AlignAndFocus doesn't necessarily rebin the data correctly
            if Process_Mode == "Set-Up":
                Rebin(InputWorkspace=unfocussedWksp,
                      Params=alignAndFocusArgs['Params'],
                      Outputworkspace=unfocussedWksp)

            NormaliseByCurrent(InputWorkspace=redWS, OutputWorkspace=redWS)

            # normalize the data as requested
            normalizationWS = self._generateNormalization(
                redWS, norm, normalizationWS)
            normalizedWS = None
            if normalizationWS is not None:
                normalizedWS = basename + '_nor'
                Divide(LHSWorkspace=redWS,
                       RHSWorkspace=normalizationWS,
                       OutputWorkspace=normalizedWS)
                ReplaceSpecialValues(Inputworkspace=normalizedWS,
                                     OutputWorkspace=normalizedWS,
                                     NaNValue='0',
                                     NaNError='0',
                                     InfinityValue='0',
                                     InfinityError='0')
                progress.report('normalized')
            else:
                progress.report()

            # rename everything as appropriate and determine output workspace name
            if normalizedWS is None:
                outputWksp = redWS
            else:
                outputWksp = normalizedWS

                if norm == "Extracted from Data" and Process_Mode == "Production":
                    DeleteWorkspace(Workspace=redWS)
                    DeleteWorkspace(Workspace=normalizationWS)

            # Save requested formats
            saveDir = self.getPropertyValue("OutputDirectory").strip()
            if len(saveDir) <= 0:
                self.log().notice('Using default save location')
                saveDir = os.path.join(self.get_IPTS_Local(runnumber),
                                       'shared', 'data')
            self._save(saveDir, basename, outputWksp)

            # set workspace as an output so it gets history
            propertyName = 'OutputWorkspace_' + str(outputWksp)
            self.declareProperty(
                WorkspaceProperty(propertyName, outputWksp, Direction.Output))
            self.setProperty(propertyName, outputWksp)

            # declare some things as extra outputs in set-up
            if Process_Mode != "Production":
                prefix = 'OuputWorkspace_{:d}_'.format(i)
                propNames = [prefix + it for it in ['d', 'norm', 'normalizer']]
                wkspNames = [
                    '%s_%s_d' % (new_Tag, runnumber), basename + '_red',
                    '%s_%s_normalizer' % (new_Tag, runnumber)
                ]
                for (propName, wkspName) in zip(propNames, wkspNames):
                    if mtd.doesExist(wkspName):
                        self.declareProperty(
                            WorkspaceProperty(propName, wkspName,
                                              Direction.Output))
                        self.setProperty(propName, wkspName)