Commit 5389c37f authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: readme

parent d3d5ce42
......@@ -61,7 +61,7 @@ If you are using ``pip``, you need to install a few additional dependencies::
pip install fmrib-unpack[demo]
You can then start the demo by running ``funpack_demo``.
You can then start the demo by running ``fmrib_unpack_demo``.
.. note:: The introductory notebook uses ``bash``, so is unlikely to work on
......@@ -74,16 +74,21 @@ Usage
General usage is as follows::
funpack [options] output.tsv input1.tsv input2.tsv
fmrib_unpack [options] output.tsv input1.tsv input2.tsv
You can get information on all of the options by typing ``funpack --help``.
You can get information on all of the options by typing ``fmrib_unpack --help``.
The `fmrib_unpack` command was called `funpack` in older versions of
FUNPACK, but was changed to `fmrib_unpack` in 3.0.0 to avoid a naming
conflict with an `unrelated software package
<https://heasarc.gsfc.nasa.gov/fitsio/>`_.
Options can be specified on the command line, and/or stored in a configuration
file. For example, the options in the following command line::
funpack \
fmrib_unpack \
--overwrite \
--write_log \
--icd10_map_file icd_codes.tsv \
......@@ -103,7 +108,7 @@ Could be stored in a configuration file ``config.txt``::
And then executed as follows::
funpack -cfg config.txt output.tsv input1.tsv input2.tsv
fmrib_unpack -cfg config.txt output.tsv input1.tsv input2.tsv
Features
......@@ -134,7 +139,8 @@ Built-in rules
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:
the following files (the `funpack/` directory is located in your Python
environment directory):
* ``funpack/configs/fmrib/datacodings_*.tsv``: Cleaning rules for data codings
* ``funpack/configs/fmrib/variables_*.tsv``: Cleaning rules for individual
......@@ -145,7 +151,7 @@ the following files:
You can use these rules by using the FMRIB configuration profile::
funpack -cfg fmrib output.tsv input.tsv
fmrib_unpack -cfg fmrib output.tsv input.tsv
You can customise or replace these files as you see fit. You can also pass
......@@ -326,6 +332,7 @@ before calling FUNPACK, like so::
export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES
fmrib_unpack ...
Citing
......
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