AutoReduction Configuration#

Here follows is a template autoreduction configuration file in json format,

{
    "Cycle": "2025-1_11A_CAL",
    "SampleEnvironment": "PAC",
    "OverwriteUserJsonFile": "Y",
    "ConfigFile": {
        "PAC": "PAC_default.json",
        "HTJANIS": "HTJANIS_default.json",
        "LTJANIS": "LTJANIS_default.json",
        "OC": "OC_default.json",
        "MICAS": "MICAS_default.json",
        "MICAS-33420": "MICAS_33420.json",
        "MICAS-32378": "MICAS_32378.json",
        "AGES": "AGES_default.json",
        "JANIS_GAS_noscale": "JANIS_GAS_noscale.json",
        "JANIS_GAS": "JANIS_GAS.json",
        "MAG": "MAG_default.json",
        "MAG-He3": "MAG_He3_default.json"
    },
    "Notes": "",
    "SNSPowderRedAbsCacheDir": "/SNS/PG3/shared/autoreduce/snspdr_abs_ms",
    "Comment-1": "Entries below are for MantidTotalScattering",
    "ClientID": ".....",
    "Secret": ".....",
    "TokenURL": "https://snsapp1.sns.ornl.gov/xprod_ro/proposal_production/oauth/token",
    "IPTSURL": "https://snsapp1.sns.ornl.gov/xprod_ro/proposal_production/sec_smpl/getSampleDetailsByIPTS/",
    "ONCatID": ".....",
    "ONCatSecret": ".....",
    "CacheDir": "/SNS/PG3/shared/autoreduce/mts_abs_ms",
    "EnvironmentName": "InAir",
    "InstrumentGeometryRun": "PG3_56131",
    "GroupingAllFile": "/SNS/PG3/shared/autoreduce/configs/pg3_group_all.xml",
    "SampleElementSize": 1.0,
    "ContainerElementSize": 1.0,
    "MergeRunsOptions": "2",
    "ReGenerateGrouping": 0,
    "QMaxByBank": "40.0",
    "TMinBragg": "1.0",
    "TMaxBragg": "266.0",
    "TBinBragg": "-0.0008",
    "ResampleX": -8000,
    "QParamsProcessing": "0.5,0.0005,40.",
    "OverrideUserConfig": true,
    "MTSFourierTransform": {
        "TMIN": 3000.0,
        "TMAX": 270000.0,
        "QMin": 0.5,
        "QMax": 35.0,
        "RMax": 50.0,
        "RStep": 0.01,
        "QOffset": 0.0,
        "RCutoff": 1.0,
        "Lorch": false
    },
    "ContainerPeaks": "None",
    "BkgScale": 1.0,
    "CyclePackingFrac": true,
    "ResonanceFilter": {
        "Units": "Wavelength",
        "LowerLimits": [0.3],
        "UpperLimits": [0.5]
    },
    "ReCaching": false,
    "FinalDIFC": 22585.8,
    "LastModifiedBy": "y8z",
    "LastModifiedTime": "07-16-2024 17:38:01 EST"
}

• Cycle

  Mandatory

  Specification of the run cycle. The value coming with the key should be a valid directory name under /SNS/PG3/shared/CALIBRATION/

• SampleEnvironment

  Mandatory

  Specification of the sample environment name. The value should be one of the keys in the following ConfigFile value. The Cycle, SampleEnvironment and ConfigFile keys together pin down the configuration file to use specific to the sample environment in a certain cycle. In the template presented above, the SampleEnvironment value is PAC and therefore one should be looking for the value in ConfigFile corresponding to the PAC key (namely, PAC_default.json in the example). So, the environment specific configuration to use in this case is located at,

  /SNS/PG3/shared/CALIBRATION/2025-1_11A_CAL/PAC_default.json
  

• OverwriteUserJsonFile

  Mandatory

  Whether or not to overwrite the potentially existing IPTS specific configuration file. The mechanism of central and IPTS specific configuration working together is presented in the section above. With the current key, the instrument team has the power to control whether or not to let the central configuration win over. Y is for Yes and N for No.

• ConfigFile

  Mandatory

  This specifies a dictionary pointing each sample environment to its dedicated configuration file name. As mentioned above, the value here will be used together with the Cycle and SampleEnvironment keys to pin down the configuration file to load. The configuration to load applies to only specific sample enviroments and this is why we are separating out the sample environment specific configurations.

• Notes

  Optional

  This is expected to be a single string without any white spaces (tabs or spaces). If a non-empty string is given, it will be used as part of the name for the calibration file to be used. See the sample environment specific configurations documentation below for more details.

• SNSPowderRedAbsCacheDir

  Optional

  With the abs_pre_calc routine, it is now possible to pre-calculate the absorption given a certain IPTS and the pre-calculated absorption will be saved into the specified location here. If the key is provided here, the autoreduction will try to find the pre-calculated absorption saved in the specified location and if existing, autoreduction will load it in for boosting the calculation. If the key is not provided, autoreduction will use an IPTS specific directory for absorption caching while running the reduction.

• Comment-1

  Optional

  This is just an annotation entry for the verbose purpose without any real functionality attached. It is for indicating that the configurations above the comment entry are for SNSPowderReduction and below the comemnt entry, the configurations are for MantidTotalScattering.

• ClientID

  Mandatory

  The client ID for talking to the ITEMS database.

• Secret

  Mandatory

  The secret for talking to the ITEMS database.

• TokenURL

  Mandatory

  The token URL for talking to the ITEMS database.

• IPTSURL

  Mandatory

  The IPTS URL for talking to the ITEMS database.

• ONCatID

  Mandatory

  The ONCAT ID for talking to the ONCAT database.

• ONCatSecret

  Mandatory

  The ONCAT secret for talking to the ONCAT database.

• CacheDir

  Mandatory

  Specify the cache directory for the MantidTotalScattering reduction.

• EnvironmentName

  Optional

  Name of the sample environment, Usually it is just InAir and we barely need to touch it.

• GroupingAllFile

  Optional

  The XML file specifying the grouping of all detectors. As long as there is no detector upgrade on the instrument, there is no need to change this.

• SampleElementSize

  Optional

  Cuboid size in mm for the absorption calculation for the sample.

• ContainerElementSize

  Optional

  Cuboid size in mm for the absorption calculation for the container.

• MergeRunsOptions

  Optional

  The criterion for merging different run numbers. Two options are available, 1 for using the run title with dynamic temperature information and 2 for using the run title without the dynamic temperature. The default option is 2 as usually we are not interested in the temperature fluctuation around the set point.

• ReGenerateGrouping

  Optional

  This is the key for detector grouping according to the similarity in absorption spectra as mentioned earlier. If no upgrade to the detectors, one can always stay with 0 as the input here, indicating that we don’t want to re-generate the group. For POWGEN, the grouping files and information are stored in the following directory, /SNS/PG3/shared/autoreduce/configs.

• QMaxByBank

  Mandatory

  The QMax value to be used for each of the output bank of data. If one value is given, it will be used for banks. Multiple values can be provided, separated by comma. The value should be given in a string, as presented in the example above.

• TMinBragg

  Mandatory

  The minimal TOF value for the output Bragg diffraction data for each bank.

• TMaxBragg

  Mandatory

  The maximal TOF value for the output Bragg diffraction data for each bank.

• QParamsProcessing

  Mandatory

  This is the $Q$-space binning parameters used internally for MTS data processing. Since we are going to throw away the neutron events after the data processing, we have to use a fine $Q$-space binning to make sure that we can always go with a coarser bin for the binning down the road.

• OverrideUserConfig

  Optional

  Any time the autoreduction is running, it will try to load or save the central configuration to the experiment-specific location so that later on, on the user side, they can change the parameter locally without influencing others. The default value for this flag is false, indicating that as long as the previously saved user configuration file can be found, the autoreduction routine will pick it up. If the flag is set to true, the central configuration will take the priority and after the reduction, the central configuration file will be copied into the experiment-specific location, with whatever existing configuration files there backed up to avoid losing history.

• CyclePackingFrac

  Optional

  For the autoreduction purpose, we could check the log file from MTS running, grab the suggested packing fraction and start a new reduction with the tweaked packing fraction until the convergence of the packing fraction. This flag controls whether we want to perform such a loop. The default option is true, but in some cases, due to the poor data quality, the loop may get stuck, in which case we want to turn off the cycling.

• MTSFourierTransform

  Optional

  A dictionary should be given as the value. Here are the entries in the dictionary,

  • TMIN

    Mandatory

    This value will go into the TMin key of AlignAndFocusArgs for the sample, specifying the minimum TOF for the align-and-focus operation in microsecond.

  • TMAX

    Mandatory

    This value will go into the TMax key of AlignAndFocusArgs for the sample, specifying the maximum TOF for the align-and-focus operation in microsecond.

  • QMin

    Mandatory

    This key controls the minimal $Q$ used for Fourier transform, to obtain the PDF.

  • QMax

    Mandatory

    This key controls the maximal $Q$ used for Fourier transform, to obtain the PDF.

  • RMax

    Mandatory

    This key controls the maximal $r$ of the PDF data.

  • RStep

    Mandatory

    This key controls the interval of the PDF data.

  • QOffset

    Mandatory

    The offset in $Q$-space that we want to apply to the reduced total scattering data before the Fourier transform.

  • RCutoff

    Mandatory

    The cutoff in $r$-space regarding the Fourier filter, i.e., all signals below the cutoff will be Fourier filtered.

  • Lorch

    Mandatory

    Whether to apply the lorch smoothing algorithm for the PDF data.

• FinalDIFC

  Mandatory

  After the total scattering data processing, the data would be in $Q$-space. To obtain the Bragg diffraction data in TOF-space which can be imported into Rietveld programs for data analysis, we have to convert the $Q$-space data with some arbitrary values of DIFC for each bank of data. Here we can give the list of the DIFC values to be used for such a purpose and the aim is to keep consistent whatever conventional values that other data reduction programs were using.

• ContainerPeaks

  Optional

  With this flag, one can specify a list of peaks (in d-space) for the container in case there are Bragg peaks in the container signal that needs to be stripped off. The list should be given in a string and different peak positions should be separated with comma.

• BkgScale

  Optional

  Specify a scale factor to be multiplied onto the container background in case of over or under subtraction of the container signal.

• ResonanceFilter

  Optional

  A dictionary is expected to be provided with the key. Here are the expected entries of the dictionary,

  • Units

    Mandatory

    Specify the space in which the resonance filter parameters will be applied. Acceptable values are those in Mantid unit factor – see here.

  • LowerLimits

    Mandatory

    Specify a list of lower limits of the window within which the neutron counts are to be excluded.

  • UpperLimits

    Mandatory

    Specify a list of upper limits of the window within which the neutron counts are to be excluded. The length of the LowerLimits and UpperLimits lists should be equal to each other.