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INSTALL.md

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Installation instructions

Author: Kris Thielemans

An easy way to run the exercises is to use the SIRF Virtual Machine where SIRF has already been installed for you. Alternatively you can install SIRF yourself. Below are some brief instructions.

The exercises use Jupyter notebooks. These provide a nice GUI interface to Python. You need 2 components: the jupyter notebook server and a web browser.

SIRF Virtual Machine

We distribute a VM with SIRF and all its dependencies, please check our wiki. The VM also contains the source for the SIRF-Exercises. However, we do not include the data to restrict its file size. Therefore, please install the VM as per the instructions, start it up, open a terminal and execute the following:

  • We recommend first updating your VM

    update_VM.sh

  • Get example data

     ~/devel/SIRF-Exercises/scripts/download_data.sh -m -p

    This will be a ~2.5 GB download.

    Note that if you want to run notebooks in MR/Old_notebooks (not recommended), you will have to get some more data

    ~/devel/SIRF-Exercises/scripts/download_data.sh -m -p -o

You now have everything ready.

Check our README for more information on usage.

Installing SIRF and the exercises yourself

You will need SIRF of course. Please check the instructions on our wiki.

The SIRF-exercises themselves can just be downloaded, preferably via

mkdir ~/devel
cd ~/devel
git clone https://github.com/SyneRBI/SIRF-Exercises
cd SIRF-Exercises

adjusting the path to where you want to install the SIRF-Exercises of course.

You will need to install the additional Python dependencies needed for the exercises also

$SIRF_PYTHON_EXECUTABLE -m pip install --user -r requirements.txt

where we used the environment variable created when you follow the SIRF-SuperBuild instructions to make sure that you use a Python version which is compatible with how you compiled SIRF. This will do a "user" install - if you'd prefer a system install omit the --user flag. If you don't know what this means, use the above command.

Of course, if you've used (Ana)conda to install Python etc (and are sure SIRF was compiled with that Python version), you can use conda to install dependencies as well. Or you could still choose to use conda's pip after

conda install pip

After all this, you will need to do the steps indicated in the instructions above for the VM, after the update_VM.sh step.

Updating the exercises after installation

You can repeat clone the repository again to get any updates. However, if you made any changes to the exercises, you might want to keep those. Merging your changes and any "upstream" ones is unfortunately a bit complicated due to the file format used by jupyter notebooks. The following should work

cd SIRF-Exercises
nbstripout --install
git config --global filter.nbstripout.extrakeys '
  metadata.celltoolbar 
  metadata.language_info.codemirror_mode.version
  metadata.language_info.pygments_lexer metadata.language_info.version'
git pull

(You do not have to write the nbstripout lines on the VM, and on other systems you have to write those only once).