Transmission Workflow Algorithm

[Owen Arnold]

There is a lack of flexibility in the current quick script (and also now #8371) that the users don't like. Essentially the generation and normalisation of transmission runs is hard-coded. The algorithms/scripts both make and use the Transmission runs. It would be better to separate out the building of the Transmission runs from their usage. This would also collapse the existing ReflectometryReductionOne algorithm down by quite a bit.

• Create a new CreateTransmissionCorrection workflow algorithm. Fortunately, I knew that this work would be upon us so most of the Transmission Correction functionality is in a stand-alone method. Things like toLam may make a base algorithm.
• Make ReflectometryReductionOne use CreateTransmissionCorrection
• If the workspace 'FirstTransmissionRun' appears to be in units of wavelength. Assume that it has already been reduced and just use it as the denominator in the normalisation step. Otherwise if it's in TOF, run the TransmissionCorrection procedures. Otherwise, fall over and die (loudly).

[Owen Arnold]

refs #8589. Template for new algorithm and tests.

Changeset: e2128e7236d3895d17933187fdb438e7b54dd3a2

[Owen Arnold]

refs #8589. Create a base algorithm class.

Changeset: 8843ff2e46b881957c3513790828f336974364e4

[Owen Arnold]

refs #8589. Move common toLam to base class.

Move and make adjustments to ensure that everything is still working and that tests still pass.

Changeset: fbb8721407a278f229c12e8b8ce7671a7a9f4bc8

[Owen Arnold]

refs #8589. Move existing functions into base class.

Will still need to do some work around these yet.

Changeset: 5340581d1e4681256d642002280b95473e84bdd7

[Owen Arnold]

refs #8589. Move transmission correction code into base class.

More work will need to be done here because we yet need to separate out the making from the utilisation parts in order for this to be useful to both Correction and Reduction algorithms which use it.

Changeset: bcc2ae5d4c86faa9f3bab71e240915a6bcbce1e6

[Owen Arnold]

refs #8589. Separate make transmission method.

This method is used by current transmission run method, can also be used by Correction algorithm separately.

Changeset: 9833ce578e81d1a6f11ed7d1effd34b88cf772fe

[Owen Arnold]

refs #8589. Check spectrum numbers of input trans workspaces.

Add unit tests to demonstrate happy-paths for the CreateTransmissionWorkspace alg.

Changeset: c0035476bdc925d568cc4a38a51ca779ca79782d

[Owen Arnold]

refs #8589. Move trans corr to utilising algorithm class.

The bit that is actually applying the trans corr is not required in the base class.

Changeset: ae7bab4351315de14b3a03dffade074e6e625e0a

[Owen Arnold]

refs #8589. Call make transmission via algorithm.

This is a better strategy particularly when nested histories become possible.

Changeset: 6f05e9ce12f01cc740fdfbc403f8af7a91a78ad2

[Owen Arnold]

refs #8589. Make transmission runs not needed on base.

Make transmission runs can be private to the creation algorithm now that the workflow algorithm is calling the creational algorithm rather than using a shared method on the base class.

Changeset: e63d50f4cf3a9590d31fca12cd37ca51d4227bbb

[Owen Arnold]

refs #8589. Use rather than make transmission workspaces.

Use rather than make a transmission workspace if the units are in wavelength.

Changeset: 772363c95337f00ef53729b5d829d304b4f445d0

[Owen Arnold]

refs #8589. Remove unused test files.

Changeset: 19f56949194af1749d233e189fb49d4a69a59dee

[Owen Arnold]

refs #8589. Improve documentation where possible.

Changeset: d05a1240d3c2bdbb71a533609d3990a18ffcb93c

[Owen Arnold]

refs #8589. Bad property names.

Stitching is actually happening with workspaces in wavelength not in Q. Parameter names and documentation needs to reflect this.

Changeset: fe9ac6f1f913b5ce9c075658a205f0b6c95809c1

[Owen Arnold]

Tester. The algorithms now achieve all of the above stated aims. The following script shows this. With one run of ReflectometryReductionOne, we allow it to process and utilise the raw transmission runs. For the second run of the algorithm, we run Create TransmissionWorkspace first, and then pass that result in as the FirstTransmissionRun. The plot shows that the results are identical.

from mantid.simpleapi import *
from isis_reflectometry import quick
reload(quick)

class ReflectometryQuick(object):
  
    def runTest(self):
        defaultInstKey = 'default.instrument'
        defaultInstrument = config[defaultInstKey]
        
        config[defaultInstKey] = 'INTER'
        LoadISISNexus(Filename='13463', OutputWorkspace='13463')
        LoadISISNexus(Filename='13464', OutputWorkspace='13464')
        LoadISISNexus(Filename='13460', OutputWorkspace='13460')
    
        transmissionRuns = '13463,13464'
        runNo = '13460'
        incidentAngle = 0.7
        quick.quick(runNo, trans=transmissionRuns) 

        config[defaultInstKey] = defaultInstrument
        
        # Existing behaviour all-in-one Reflectometry Reduction and Transmission correction.
        new_IvsQ1, new_IvsLam1, thetaOut1 = ReflectometryReductionOne(InputWorkspace='13460', WavelengthMin=1.0, WavelengthMax=17.0, WavelengthStep=0.05, MonitorBackgroundWavelengthMin=15.0, 
        MonitorBackgroundWavelengthMax=17.0, I0MonitorIndex=2, MonitorIntegrationWavelengthMin=4.0, MonitorIntegrationWavelengthMax=10.0, WorkspaceIndexList=[3,4], Params=[1.5, 0.02, 17], 
        StartOverlap=10.0, EndOverlap=12.0, FirstTransmissionRun='13463', SecondTransmissionRun='13464')
        

        # Separately compute the transmission run.
        transmission = CreateTransmissionWorkspace(WavelengthMin=1.0, WavelengthMax=17.0, WavelengthStep=0.05, MonitorBackgroundWavelengthMin=15.0, 
        MonitorBackgroundWavelengthMax=17.0, I0MonitorIndex=2, MonitorIntegrationWavelengthMin=4.0, MonitorIntegrationWavelengthMax=10.0, 
        WorkspaceIndexList=[3,4], Params=[1.5, 0.02, 17], StartOverlap=10.0, EndOverlap=12.0, FirstTransmissionRun='13463', SecondTransmissionRun='13464')
        

        # Pass the transmission run into ReflectometryReductionOne.
        new_IvsQ2, new_IvsLam2, thetaOut2 = ReflectometryReductionOne(InputWorkspace='13460', WavelengthMin=1.0, WavelengthMax=17.0, WavelengthStep=0.05, MonitorBackgroundWavelengthMin=15.0, 
        MonitorBackgroundWavelengthMax=17.0, I0MonitorIndex=2, MonitorIntegrationWavelengthMin=4.0, MonitorIntegrationWavelengthMax=10.0, WorkspaceIndexList=[3,4], 
        FirstTransmissionRun=transmission)
        
        plotSpectrum([new_IvsLam1, new_IvsLam2, '13460_IvsLam'], [0])
        plotSpectrum([new_IvsQ1, new_IvsQ2, '13460_IvsQ'], [0])
        
        
test = ReflectometryQuick()
test.runTest()

[Peter Parker]

Merge remote-tracking branch 'origin/feature/8589_transmission_workflow'

Full changeset: ​0c00f6ec424d77546b604829a284ec6a65bd2b05

[Stuart Campbell]

This ticket has been transferred to github issue ​9433