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

Or you may want the nipy-data package, in which case:

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