Enable user defined sample and container geometry for abs correction #38887

Kvieta1990 · 2025-02-19T04:54:56Z

Description of work

Summary of work

With this PR, we enable user defined sample and container geometry for absorption correction. Top level changes are in place for SNSPowderReduction and accordingly necessary parameters are introduced for those bottom level algorithms concerning the setup of the absorption correction inputs. The defined sample and container geometry is finally passed to SetSample. This gives users the flexibility to define their own geometry as needed. For example, on POWGEN, some times irregular containers that are not defined in the sample environment XML file will be used for the measurement, e.g., the annular container where the sample is loaded into the hollow cylinder wall.

Also, we implement the definition of beam gauge volume for absorption correction. Without this implementation, the assumption would be that the beam size is the same as the sample size. In practice, this is often not true. In that case, the absorption correction is imperfect in principle. Detailed discussion about this is posted here.

To test:

This is the one for testing the gauge volume definition

from mantid.simpleapi import *

gauge_vol = '''<cuboid id="shape">
     <left-front-bottom-point x="0.01" y="-0.1" z="0.0"  />
     <left-front-top-point  x="0.01" y="-0.1" z="0.02"  />
     <left-back-bottom-point  x="-0.01" y="-0.1" z="0.0"  />
     <right-front-bottom-point  x="0.01" y="0.1" z="0.0"  />
   </cuboid>'''

SNSPowderReduction(
    Filename='/SNS/PG3/IPTS-34523/nexus/PG3_58812.nxs.h5',
    CalibrationFile='/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_OC_d58772_2025-02-12.h5',
    CharacterizationRunsFile='/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_char_2025_2-HighRes_OC.txt,/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_char_2025_2_OC_limit.txt',
    RemovePromptPulseWidth=50,
    Binning='-0.0008',
    BackgroundSmoothParams='5, 2',
    FilterBadPulses=90,
    ScaleData=100,
    TypeOfCorrection='SampleAndContainer',
    SampleFormula='Ba-Nb-Cr-Ru',
    MeasuredMassDensity='6.0',
    SampleGeometry={'Height': 5},
    SampleNumberDensity='0.088',
    ContainerShape='PAC06',
    GaugeVolume=gauge_vol,
    SaveAs='gsas topas and fullprof',
    OutputDirectory='/SNS/NOM/shared/tmp',
    CacheDir='/SNS/NOM/shared/tmp'
)

Here is the one for testing the geometry definition,

from mantid.simpleapi import *

sam_geo = {
    'Shape': 'HollowCylinder', 'Height': 4.0,
    'InnerRadius': 2.0,
    'OuterRadius': 3.0,
    'Center': [0.,0.,0.]
}

c_geo = {
    'Shape': 'HollowCylinderHolder',
    'Height': 4.0,
    'InnerRadius': 1.5,
    'InnerOuterRadius': 2.0,
    'OuterInnerRadius': 3.0,
    'OuterRadius': 4.0,
    'Center': [0.,0.,0.]
}

c_mat = {
    'ChemicalFormula': 'V',
    'NumberDensity': 0.072324
}

gauge_vol = '''<cuboid id="shape">
     <left-front-bottom-point x="0.01" y="-0.1" z="0.0"  />
     <left-front-top-point  x="0.01" y="-0.1" z="0.02"  />
     <left-back-bottom-point  x="-0.01" y="-0.1" z="0.0"  />
     <right-front-bottom-point  x="0.01" y="0.1" z="0.0"  />
   </cuboid>'''

SNSPowderReduction(
    Filename='/SNS/PG3/IPTS-34523/nexus/PG3_58812.nxs.h5',
    CalibrationFile='/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_OC_d58772_2025-02-12.h5',
    CharacterizationRunsFile='/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_char_2025_2-HighRes_OC.txt,/SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PG3_char_2025_2_OC_limit.txt',
    RemovePromptPulseWidth=50,
    Binning='-0.0008',
    BackgroundSmoothParams='5, 2',
    FilterBadPulses=90,
    ScaleData=100,
    TypeOfCorrection='SampleAndContainer',
    SampleFormula='Ba-Nb-Cr-Ru',
    MeasuredMassDensity='6.0',
    SampleGeometry=sam_geo,
    SampleNumberDensity='0.088',
    ContainerGeometry=c_geo,
    ContainerMaterial=c_mat,
    GaugeVolume=gauge_vol,
    SaveAs='gsas topas and fullprof',
    OutputDirectory='/SNS/NOM/shared/tmp',
    CacheDir='/SNS/NOM/shared/tmp'
)

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…ntid into abs_can_geo_def

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peterfpeterson · 2025-02-20T19:44:05Z

Framework/PythonInterface/mantid/utils/absorptioncorrutils.py

        )

+    if beam_height != Property.EMPTY_DBL and not gauge_vol:
+        gauge_vol = """<cuboid id="shape">


This is strange in a way similar to the DefineGaugeVolume user docs. I think it is configured that

front-back is x-dimension

left/right is y-dimension (beam height)

top/bottom is z-dimension

It would be good to also add in the beam width for the dimension that has that

Adding a comment explaining that will help future people who see this.

The DefineGaugeVolume user docs is indeed a bit confusing in the explanation of how the gauge volume is defined. Here are several comments,

For the cuboid volume definition, I created an image to demonstrate the idea,

Ideally, indeed the gauge volume could be defined as above a a cuboid and Mantid then worries about constructing the intersection area between the sample and the defined gauge volume. However, the construction of the intersection area is not implemented yet. So, we cannot go with this route.

However, the gauge volume can be defined as with the same shape as the sample, e.g., cylinder or hollow cylinder and current implementation can meet our need without problems. We do need some further implementation in this PR to define the gauge volume for the sample and container separately.

The implementation for SampleOnly and SampleAndContainer method is straightforward -- just define the gauge volume twice here

For the PaalmanPingsAbsorptionCorrection method, I am not sure how to do that -- the same principle applies but I am not so familiar with the CPP codes.

At ISIS we are also interested in starting to use DefineGaugeVolume with other attenuation algorithms such as MonteCarloAbsoption for use on our engineering beamline ENGIN-X. For us we would need to consider the case of when the gauge volume is not wholly occupied by the sample, both for attenuation correction and normalising by the illuminated sample volume. If you do implement this let us know! Not sure how this fits in with your plans? Happy to discuss!

enable user defined sample and container geometry for abs correction

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Kvieta1990 self-assigned this Feb 19, 2025

pre-commit-ci bot and others added 3 commits February 19, 2025 04:57

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add in release doc

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Merge branch 'abs_can_geo_def' of https://github.com/mantidproject/ma…

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…ntid into abs_can_geo_def

Kvieta1990 added Diffraction Issues and pull requests related to diffraction Powder Issues and pull requests related to powder diffraction Absorption Corrections Issues and pull requests related to absorption corrections labels Feb 19, 2025

fix logic

0f49dc6

sf1919 added this to the Release 6.13 milestone Feb 19, 2025

Kvieta1990 and others added 2 commits February 19, 2025 09:46

fix beam height issue

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Kvieta1990 requested a review from peterfpeterson February 19, 2025 15:10

remove redundant checks

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peterfpeterson changed the title ~~enable user defined sample and container geometry for abs correction~~ Enable user defined sample and container geometry for abs correction Feb 20, 2025

peterfpeterson reviewed Feb 20, 2025

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fix gauge volume issue

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Enable user defined sample and container geometry for abs correction #38887

Enable user defined sample and container geometry for abs correction #38887

Kvieta1990 commented Feb 19, 2025 •

edited by peterfpeterson

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peterfpeterson Feb 20, 2025

Kvieta1990 Feb 21, 2025

RichardWaiteSTFC Feb 21, 2025

Enable user defined sample and container geometry for abs correction #38887

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Enable user defined sample and container geometry for abs correction #38887

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Kvieta1990 commented Feb 19, 2025 • edited by peterfpeterson Loading

Description of work

Summary of work

To test:

This is the one for testing the gauge volume definition

Here is the one for testing the geometry definition,

Reviewer

Code Review

Functional Tests

Gatekeeper

peterfpeterson Feb 20, 2025

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Kvieta1990 Feb 21, 2025

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Kvieta1990 commented Feb 19, 2025 •

edited by peterfpeterson

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