.. algorithm::

.. summary::

.. relatedalgorithms::

.. properties::

Description
-----------

The main equation Bilby is using for the :math:`I(Q)` calculation is the following:

.. math:: I(Q)=\frac{1}{d_{sam}}.\frac{\sum_{R, \lambda \subset Q}C_{sam,corr}(R,\lambda)}{M \sum_{R,\lambda \subset Q}T_{corr}(R, \lambda)\frac{I_{empty\_beam}(\lambda)}{M_{empty\_beam}att_{empty\_beam}}\Omega(R)Det_{flood}(R)}

Where :math:`C_{sam, corr}` is the measured counts per pixel per wavelength,
:math:`I_{empty\_beam}` is the intensity of the empty beam collected for :math:`M_{empty\_beam}` time,
M is a time measure for the data collection, :math:`att_{empty\_beam}` is attenuation factor,
:math:`\Omega(R)` is solid angle, :math:`Det_{flood}` is a detector response function,
:math:`T_{corr}` is the sample transmission, and :math:`d_{sam}` is the sample thickness.

Details are described in the paper [#Sokolova]_.
The core algorithms the BilbySANSDataProcessor is utilising are :ref:`Q1D <algm-Q1D>` and :ref:`TOFSANSResolutionByPixel <algm-TOFSANSResolutionByPixel>`.
Please refer to those pages for details of the input parameters.
The unit of the output workspace is 1/cm. Absolute scale calibration done relatively to the empty beam transmission measurements.

Usage
-----

See https://github.com/hortica/Mantid_Bilby/tree/master/example_data_reduction_settings page to download a set of the test input data.

Please note, currently we do not have a User Interface, so we are working with csv lists.

The steps to make the Bilby data reduction work are listed below:

* Two csv files, similar to (input_csv_example.csv and mantid_reduction_settings_example.csv) should be created during the experiment; the names can be different, the format (especially the top line in each) must stay the same
* Download Mantid from http://download.mantidproject.org/
* Add the folder with your \*.tar files AND  the two csv files (input_csv_example.csv and mantid_reduction_settings_example.csv) to the path (added to “Mantid User Directories”)
   * To keep it simple, one can put tar and csv files in one folder, but you can add as many folders on the paths as you want
* Open the Script menu in Mantid: press “View”, and then “Script window”; alternalively just press F3
* The script below shows an example script to run the Bilby reduction the reduction_settings_file options should be changed to the correct .csv file file and save_files set to true.
* Run the reducer, Execute -> Execute All in the Menu
   * All output 1D files will be saved in the folder you define in the mantid_reduction_settings_example.csv

.. testcode:: BilbyReductionExample

    from BilbyReductionScript import RunBilbyReduction
    run_bilby_reduction = RunBilbyReduction('mantid_reduction_settings_example.csv', '0', '0', 'shift_assembled.csv', False)
    output_workspace, transmission_fit = run_bilby_reduction.run_bilby_reduction()

.. testoutput::  BilbyReductionExample

   scale, aka attenuation factor 0.0029

References
----------

.. [#Sokolova] A. Sokolova, A. E. Whitten, L. de Campo, J. Christoforidis, A. Eltobaji, J. Barnes, F. Darmann and A. Berry (2019). Journal of Applied Crystallography Volume 52 (1)
          `doi: 10.1107/S1600576718018009 <https://doi.org/10.1107/S1600576718018009>`_

.. sourcelink::

.. categories::