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.. _data-files:
######################
Optional data packages
######################
The source code has some very small data files to run the tests with,
but it doesn't include larger example data files, or the all-important
brain templates we all use. You can find packages for the optional data
and template files at http://nipy.org/data-packages.
If you don't have these packages, then, when you run nipy installation,
you will probably see messages pointing you to the packages you need.
*********************************************
Data package installation as an administrator
*********************************************
The installation procedure, for now, is very basic. For example, let us
say that you need the 'nipy-templates' package at
http://nipy.org/data-packages/nipy-templates-0.3.tar.gz
. You simply download this archive, unpack it, and then run the standard
``python setup.py install`` on it. On a unix system this might look
like::
# curl -L flag to follow redirect; can also use wget
curl -OL http://nipy.org/data-packages/nipy-templates-0.3.tar.gz
tar zxvf nipy-templates-0.3.tar.gz
cd nipy-templates-0.3
sudo python setup.py install
This is for the `nipy-templates` package; there is also a `nipy-data` package,
for which the equivalent would be:
curl -OL http://nipy.org/data-packages/nipy-data-0.3.tar.gz
On windows, download the file, extract the archive to a folder using the
GUI, and then, using the windows shell or similar::
cd c:\path\to\extracted\files
python setup.py install
*******************************************
Non-administrator data package installation
*******************************************
The simple ugly manual way
==========================
These are instructions for using the command line in Unix. You can do similar
things from Windows powershell.
* Locate your nipy user directory from the output of this::
python -c 'import nibabel.data; print(nibabel.data.get_nipy_user_dir())'
Call that directory ``<nipy-user>``. Let's imagine that, for you, this is
``~/.nipy``.
* Make a subdirectory ``nipy`` in your ``<nipy-user>`` directory. In
Unix you could use::
mkdir -p ~/.nipy/nipy
where the ``-p`` flag tells Unix to make any necessary parent directories.
* Go to http://nipy.org/data-packages
* Download the latest *nipy-templates* and *nipy-data* packages, to some
directory. You can do this via the GUI, or on the command line (in Unix)::
cd ~/Downloads
curl -OL http://nipy.org/data-packages/nipy-templates-0.3.tar.gz
curl -OL http://nipy.org/data-packages/nipy-data-0.3.tar.gz
* Unpack both of these::
tar zxvf nipy-data-0.3.tar.gz
tar zxvf nipy-templates-0.3.tar.gz
* After you have unpacked the templates, you will have a directory called
something like ``nipy-templates-0.3``. In that directory you should see a
subdirectory called ``templates``. Copy / move / link the ``templates``
subdirectory into ``<nipy-user>/nipy``, so you now have a directory
``<nipy-user>/nipy/templates``. From unpacking the data, you should also
have a directory like ``nipy-data-0.3`` with a subdirectory ``data``. Copy
/ move / link that ``data`` directory into ``<nipy-user>/nipy`` as well.
For example::
cp -r nipy-data-0.3/data ~/.nipy/nipy
cp -r nipy-templates-0.3/templates ~/.nipy/nipy
* Check whether that worked. Run the following command from the shell::
python -c 'import nipy.utils; print(nipy.utils.example_data, nipy.utils.templates)'
It should show something like::
(<nibabel.data.VersionedDatasource object at 0x101f8e410>, <nibabel.data.VersionedDatasource object at 0x10044b110>)
If it shows ``Bomber`` objects instead, something is wrong. Go back and
check that you have the nipy home directory right, and that you have
directories ``<nipy-user>/nipy/data`` and ``<nipy-user>/nipy/templates>``,
and that each of these two directories have a file ``config.ini`` in them.
The more general way
====================
The commands for the system install above assume you are installing into the
default system directories. If you want to install into a custom directory,
then (in python, or ipython, or a text editor) look at the help for
``nibabel.data.get_data_path()`` . There are instructions there for pointing
your nipy installation to the installed data.
On unix
-------
For example, say you installed with::
cd nipy-templates-0.3
python setup.py install --prefix=/home/my-user/some-dir
Then you may want to do make a file ``~/.nipy/config.ini`` with the
following contents::
[DATA]
path=/home/my-user/some-dir/share/nipy
On windows
----------
Say you installed with (windows shell)::
cd nipy-templates-0.3
python setup.py install --prefix=c:\some\path
Then first, find out your home directory::
python -c "import os; print os.path.expanduser('~')"
Let's say that was ``c:\Documents and Settings\My User``. Then, make a
new file called ``c:\Documents and Settings\My User\_nipy\config.ini``
with contents::
[DATA]
path=c:\some\path\share\nipy
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