Commit 664cb537 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: funpack -> FUNPACK; tweak matlab code

parent 2c50d08c
``funpack`` - the FMRIB UKBioBank Normalisation, Processing And Cleaning Kit
**FUNPACK** - the FMRIB UKBioBank Normalisation, Processing And Cleaning Kit
============================================================================
......@@ -16,15 +16,15 @@
:target: https://git.fmrib.ox.ac.uk/fsl/funpack/commits/master/
``funpack`` is a Python library for pre-processing of UK BioBank data.
**FUNPACK** is a Python library for pre-processing of UK BioBank data.
``funpack`` is developed at the Wellcome Centre for Integrative
Neuroimaging (WIN@FMRIB), University of Oxford. ``funpack`` is in no way
endorsed, sanctioned, or validated by the `UK BioBank
FUNPACK is developed at the Wellcome Centre for Integrative Neuroimaging
(WIN@FMRIB), University of Oxford. FUNPACK is in no way endorsed,
sanctioned, or validated by the `UK BioBank
<https://www.ukbiobank.ac.uk/>`_.
``funpack`` comes bundled with metadata about the variables present in UK
FUNPACK comes bundled with metadata about the variables present in UK
BioBank data sets. This metadata can be obtained from the `UK BioBank
online data showcase <https://biobank.ctsu.ox.ac.uk/showcase/index.cgi>`_
......@@ -33,7 +33,7 @@ Installation
------------
Install ``funpack`` via pip::
Install FUNPACK via pip::
pip install fmrib-unpack
......@@ -50,8 +50,8 @@ Introductory notebook
The ``funpack_demo`` command will start a Jupyter Notebook which introduces
the main features provided by ``funpack``. To run it, you need to install a
few additional dependencies::
the main features provided by FUNPACK. To run it, you need to install a few
additional dependencies::
pip install fmrib-unpack[demo]
......@@ -112,9 +112,9 @@ Customising
-----------
``funpack`` contains a large number of built-in rules which have been
specifically written to pre-process UK BioBank data variables. These rules are
stored in the following files:
FUNPACK contains a large number of built-in rules which have been specifically
written to pre-process UK BioBank data variables. These rules are stored in
the following files:
* ``funpack/data/variables_*.tsv``: Cleaning rules for individual variables
......@@ -124,9 +124,9 @@ stored in the following files:
You can customise or replace these files as you see fit. You can also pass
your own versions of these files to ``funpack`` via the ``--variable_file``,
your own versions of these files to FUNPACK via the ``--variable_file``,
``--datacoding_file``, ``--type_file`` and ``--processing_file`` command-line
options respectively. ``funpack`` will load all variable and datacoding files,
options respectively. FUNPACK will load all variable and datacoding files,
and merge them into a single table which contains the cleaning rules for each
variable.
......@@ -138,7 +138,7 @@ Output
------
The main output of ``funpack`` is a plain-text tab-delimited[*]_ file which
The main output of FUNPACK is a plain-text tab-delimited[*]_ file which
contains the input data, after cleaning and processing, potentially with
some columns removed, and new columns added.
......@@ -150,7 +150,7 @@ file.
You can use any tool of your choice to load this output file, such as Python,
MATLAB, or Excel. It is also possible to pass the output back into
``funpack``.
FUNPACK.
.. [*] You can change the delimiter via the ``--tsv_sep`` / ``-ts`` option.
......@@ -167,7 +167,7 @@ Loading output into MATLAB
.. _table: https://uk.mathworks.com/help/matlab/ref/table.html
If you are using MATLAB, you have several options for loading the ``funpack``
If you are using MATLAB, you have several options for loading the FUNPACK
output. The best option is |readtable|_, which will load column names, and
will handle both non-numeric data and missing values. Use ``readtable`` like
so::
......@@ -179,7 +179,8 @@ The ``readtable`` function returns a |table|_ object, which stores each column
as a separate vector (or cell-array for non-numeric columns). If you are only
interested in numeric columns, you can retrieve them as an array like this::
rawdata = data(:, vartype('numeric')).Variables;
data = data(:, vartype('numeric'));
rawdata = data.Variables;
The ``readtable`` function will potentially rename the column names to ensure
......@@ -226,5 +227,5 @@ Citing
------
If you would like to cite ``funpack``, please refer to its `Zenodo page
If you would like to cite FUNPACK, please refer to its `Zenodo page
<https://doi.org/10.5281/zenodo.1997626>`_.
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