=========
Tutorials
=========

This page contains tutorials on how to use Anri.

Crystallography
===============
.. nbgallery::

    crystallography

.. _tut_geom:

Geometry
========

Goniometer
----------

Anri currently uses the FABLE geometry definitions for converting to and from detector, laboratory and sample coordinate systems.
Please see the included :download:`FABLE geometry document<./Fable_Geometry_version_1.0.8.pdf>` for their definitions.

As that document isn't perfectly descriptive, I'll try to describe slightly more what convention we use.
We use a right-handed coordinate system. With no goniometer rotations (all angles zero), the $\omega$ rotation axis (vertical) defines our $Z$ direction. The dty stage defines the $Y$ axis, and the $X$ axis (approximately down-beam) is perpendicular to $Y$ and $Z$.
If you are the beam, looking towards the detector from the source, the $Y$ axis points to the left.

Our goniometer stack is as follows::

    omega - roll around Z axis
    chi - roll around X axis
    wedge - roll around Y axis (in ImageD11 this has a negative sign, so we copy that too)
    dty stage - horizontal translation. Defines Y axis.
    Hutch floor

General rotation functions like :func:`anri.geom.rot_z` work thusly. 
Imagine the most basic stage, with a single rotation about $Z$. 
We want to generate a rotation matrix that encodes the pose of the stage. 
When we receive the matrix $\matr{R_z}$, it is applied like this:

$$\matr{R_z} \cdot \vec{v_{\text{sample}}} = \vec{v_{\text{lab}}}$$

Detector
--------

Something about detector space.

.. nbgallery::
    
    detector_geometry
    goniometer_geometry

Forward Modeling
=================

There's a very basic demonstration of how to perform a forward model with Anri.

.. nbgallery::
    
    forward_model_simple
    forward_model_covariance