Add initial documentation
Add synthetic data tutorial Add read the docs setup
This commit is contained in:
94
source/index.rst
Normal file
94
source/index.rst
Normal file
@ -0,0 +1,94 @@
|
||||
.. AMBER documentation master file, created by
|
||||
sphinx-quickstart on Fri Apr 11 10:48:14 2025.
|
||||
You can adapt this file completely to your liking, but it should at least
|
||||
contain the root `toctree` directive.
|
||||
|
||||
AMBER documentation
|
||||
===================
|
||||
|
||||
This is the documentation for the **A** lgorithm for **M** ultiplexing spectrometer
|
||||
**B** ackground **E** stimation with **R** otation-independence **AMBER** which is a method to estimate and background within 3D data sets.
|
||||
|
||||
This software is the result of the collaboration between the instrument responsible at the `CAMEA <https://www.psi.ch/en/sinq/camea>`_ beamline at SINQ, at the
|
||||
`Paul Scherrer Institut <https://psi.ch/>`_ with the `Swiss Data Science Center <https://www.datascience.ch/>`_ through the "Data Science for Multiplexing Spectrometers" (DS4MS) project supported by
|
||||
the fifth call for Collaborative Research Data Science Projects.
|
||||
|
||||
|
||||
Badges
|
||||
------
|
||||
|
||||
.. image:: https://gitea.psi.ch/lass_j/AMBER/actions/workflows/test.yaml/badge.svg
|
||||
:width: 200
|
||||
:alt: Test Status
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Installation
|
||||
------------
|
||||
Installation can be done through PyPI using
|
||||
|
||||
.. code-block::
|
||||
|
||||
python -m pip install AMBER
|
||||
|
||||
Alternatively, the newest version can be installed directly from the source repository through
|
||||
|
||||
.. code-block::
|
||||
|
||||
python -m pip install git https://gitea.psi.ch/lass_j/AMBER.git@master
|
||||
|
||||
|
||||
General Introduction
|
||||
--------------------
|
||||
|
||||
|
||||
**AMBER** has been developed with multiplexing neutron spectrometers in mind, i.e. a novel version of the triple axis instrument which acquires multiple data points simultaneously.
|
||||
However, the algorithm is more general and can be utilized on data with other origins.
|
||||
|
||||
The main requirements of the data are
|
||||
|
||||
#. Rotation independence of the background in two out of three directions.
|
||||
#. Smooth change of background along all directions
|
||||
#. The signal is sparse but continuous in all directions
|
||||
|
||||
**AMBER** minimizes the following cost function for the signal and background given the set of parameters :math:`\lambda`, :math:`\beta`, and :math:`\mu` on a voxelated data set:
|
||||
|
||||
.. math::
|
||||
\min_{X,b} \frac{1}{2}\lVert Y-X-\mathcal{R}b\rVert_{2}^2+\lambda\vert| X |\vert_{1} +\frac{\beta}{2} \mathrm{Tr} \left( b^T L_{b} b \right) +\frac{\mu}{2} \boldsymbol{1}_{n_x}^TX^T L_{\omega} X\boldsymbol{1}_{n_y}
|
||||
|
||||
where :math:`Y`, :math:`X`, and :math:`b` are the measured signal, the subtracted signal and the rotation independent background, respectively. :math:`\mathcal{R}` is a rotation operator taking
|
||||
the radial :math:`b` to the full space. These three parameters constitute the fitting term while the rest are denoted penalty terms. :math:`\lambda` controls the weighing of sparcity of the subtracted signal gauge through the L-1 norm
|
||||
:math:`\vert| X |\vert_{1}`, :math:`\beta` controls the smoothness of the background while :math:`\mu` the smoothness of the subtracted signal.
|
||||
|
||||
For further details, see the the paper.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Documentation & Tutorials
|
||||
-------------------------
|
||||
|
||||
For **AMBER** the following tutorials have been created
|
||||
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
:caption: Contents:
|
||||
|
||||
|
||||
tutorials/index.rst
|
||||
|
||||
|
||||
Contribute
|
||||
----------
|
||||
|
||||
|
||||
|
||||
Contact
|
||||
-------
|
||||
|
||||
|
Reference in New Issue
Block a user