.. _indra-waxs-data-reduction:
.. _reduce_WAXS_data_procedure:
.. _reduce_WAXS_data_panel:

.. index::
    Indra; Reduce WAXS data
    Indra; WAXS data reduction

Reduce WAXS data
================

When you collect data on the USAXS instrument, data are saved in folders named
using the spec file naming convention: ``MM_DD_userName``. When USAXS data are
collected, a subfolder with the suffix ``_usaxs`` is created; for SAXS data the
suffix is ``_saxs``; for WAXS data it is ``_waxs``.

.. Figure:: media/USAXSComputerDataArrangement.jpg
   :align: center
   :width: 480px

Reduced WAXS data arrangement
------------------------------

After reducing WAXS data, the Igor experiment contains WAXS data in
``root:WAXS:Samplename``, using the ``QRS`` naming
:ref:`system <important.QRS>`. To browse the experiment, use the Data Browser
(Ctrl-B or Cmd-B).

.. Figure:: media/WAXSIgorDataArrangement.jpg
   :align: center
   :width: 480px

Folders ending in ``_C`` contain pinhole-collimated data reduced at the highest
possible Q resolution, as required for WAXS.

.. index::
    Indra; WAXS data reduction panel

WAXS data reduction
-------------------

Data reduction uses the :ref:`Nika package <Introduction_Nika>`. Ensure Nika
is :ref:`installed <Installation>`. Select "*Load Nika 2D SAS macros*" from
the Macros menu, or load "*USAXS, Irena and Nika*" to load all three packages.
This creates the SAS2D menu. From the "*Instrument Configurations*" menu in
SAS2D, select "*APS USAXS-SAXS-WAXS*". This opens the instrument
configuration panel for Nika.

.. Figure:: media/WAXSReductionConfig.jpg
   :align: left
   :width: 500px
   :figwidth: 820px

Select (or keep selected) the "*WAXS*" checkbox and follow the on-screen
instructions in red. Keep other checkboxes at their defaults. The first step
is to click "*Set default settings*", which opens a file dialog. Navigate to
your WAXS data folder and select any data file from your samples (assuming no
geometry changes within the folder). Click Open.

.. Figure:: media/WAXSSelectNXDataFile.jpg
   :align: left
   :width: 500px
   :figwidth: 820px

Nika reads calibration values from the selected file and performs the following
steps automatically:

1. All instrument parameters are read and inserted into the appropriate Nika
   fields.
2. Nika opens the selected image and displays it.
3. Nika sets the correct calibration checkboxes and inserts the appropriate
   lookup function names for sample thickness, transmission, and normalization.
4. **Mask:** Depending on the "*Mask Less sensitive pixels*" checkbox, Nika
   creates one of two masks. When unchecked (default), a mask covering only
   the detector edges and the gap between tiles is applied. When checked,
   pixels between detector chips — which are typically ~1% less sensitive —
   are also masked. See :ref:`Impact of different mask selection
   <reduce_WAXS_data_mask>` below.
5. **Important:** By default, Nika uses Q as the x-axis, which is useful for
   merging USAXS+SAXS+WAXS data. Two-theta or d-spacing can be selected
   instead. Note that both the Diffraction tool in Irena and the GSAS-II
   export function convert any x-axis to two-theta automatically, so the
   x-axis choice here does not affect downstream use with those tools.
6. Nika displays the Blank selection tab, where you select the appropriate
   empty/blank file for your samples.

Select the correct blank file — right-click in the panel and use "*Match Blank*"
if needed. Double-click the file or select it and click "*Load Empty*".

.. Figure:: media/WAXSBlankSelection.jpg
   :align: left
   :width: 500px
   :figwidth: 820px

The blank file is loaded and displayed. Select the appropriate blank for each
group of samples and update it whenever geometry or sample conditions change.

.. Figure:: media/WAXSSampleBlankLoaded.jpg
   :align: left
   :width: 700px
   :figwidth: 820px

Sample and blank are displayed side by side for comparison.

Select the sample file(s) to process and click "*Process Images*". Nika
processes all selected files.

.. Figure:: media/WAXSProcessedDataImg.jpg
   :align: left
   :width: 700px
   :figwidth: 820px

.. _reduce_WAXS_data_mask:

Impact of different mask selection
-----------------------------------

Depending on data dynamic range, noise, and overall intensity, pixels at the
edges of detector chip tiles can sometimes affect data quality. This is common
for Pilatus detectors over time and at certain X-ray energies. Dectris
calibrates detector sensitivity at specific energies, but this calibration
degrades over time and at other energies. Masking these slightly lower-
sensitivity pixels trades Q resolution for data quality. The following image
shows data without and with masking of less-sensitive pixels:

.. Figure:: media/WAXSimpactOfLessSensitivePixels.jpg
   :align: left
   :width: 700px
   :figwidth: 820px

And here is how the corresponding mask appears:

.. Figure:: media/WAXSMaskedLessSensitivePixels.jpg
   :align: left
   :width: 400px
   :figwidth: 820px