Add documentation.

CHANGELOG.rst

@@ -3,6 +3,8 @@ This document contains the FSL-MRS release history in reverse chronological orde
 1.1.3 (TBC)
 ------------------------------
 - Added mrs_tools script. Replaces mrs_vis and mrs_info. Adds split/merge/reorder functionality.
+- Added basis_tools script. Tools for manipulating (shifting, scaling converting, and adding to) basis sets.
+- Under the hood refactor of basis, MRS and MRSI classes.
 
 1.1.2 (Friday 16th April 2021)
 ------------------------------

README.md

@@ -53,6 +53,8 @@ After installation see the [quick start guide](https://open.win.ox.ac.uk/pages/f
 : simulate basis spectra
 - **mrs_tools**
 : Collection of tools for NIfTI-MRS. Includes quick visualisation and information.
+- **basis_tools**
+: Collection of tools for manipulating basis sets.
 - **svs_segment & mrsi_segment**
 : Run tissue segmentation for SVS/MRSI from T1 image.
 

docs/user_docs/basis_tools.rst

+.. _basis_tools:
+
+Basis Spectra Manipulation
+==========================
+
+basis_tools
+-----------
+The :code:`basis_tools` script provides the user with tools for manipulating basis spectra in the FSL-MRS JSON format.
+
+Provide one of the following subcommands with :code:`basis_tools` to convert, scale, add to or shift basis spectra.
+
+info
+****
+| *Example* :code:`basis_tools info path/to/my/basis`
+| Provides a short summary of the contents of the basis set.
+
+vis
+***
+| *Example* :code:`basis_tools vis path/to/my/basis --ppmlim 0.2 4.2`
+| Provides visualisation of the basis set.
+
+convert
+*******
+| *Example* :code:`basis_tools convert path/to/my/lcmbasis.BASIS path/to/my/fslbasis`
+| Convert LCModel (.Basis) or JMRUI format basis sets to FSL-MRS (.json) format.
+
+add
+***
+| *Example* :code:`basis_tools add --scale --name my_new_basis my_new_basis.json path/to/my/fslbasis`
+| Add a json formatted basis spectrum to an existing basis set.
+
+shift
+*****
+| *Example* :code:`basis_tools shift path/to/my/fslbasis NAA 1.0 path/to/my/edited_fslbasis`
+| Shift a basis spectrum on the chemical shift axis.
+
+scale
+*****
+| *Example* :code:`basis_tools shift path/to/my/fslbasis NAA path/to/my/scaled_fslbasis`
+| Rescale a basis spectrum to the mean of all other basis spectra (or to specified target :code:`--target_scale`.
\ No newline at end of file

docs/user_docs/index.rst

@@ -25,6 +25,7 @@ If this is your first experience with FSL-MRS, get started with the :ref:`Quick
    quantitation
    macromolecules
    simulation
+   basis_tools
    visualisation
    constants
    troubleshooting