This plugin allows users to integrate NeuroPoly's shimming-toolbox application with the FSLeyes GUI. You can read the Shimming Toolbox Documentation for more information, or view the Shimming Toolbox GitHub Repo to see the source code.
In the fsleyes-plugin-shimming-toolbox folder, run:
make install
Now, you can open the FSLeyes GUI from any environment by running:
shimming-toolbox
The FSLeyes GUI should open. Once it is open, select from the toolbar:
Settings --> OrthoView --> Shimming Toolbox
The ShimmingToolbox plugin should open as a panel.
We can use Docker to spin up a Linux instance and test our install procedure in a clean
environment. You will need to install Docker on your computer first: https://www.docker.com/products/docker-desktop
To create our testing container, we will first build an image called fpst:latest:
docker build --tag fpst:latest .
Once our image is built, we want to remove any running instances of the container:
docker rm --force fpst
Then, we can create a container from our fpst:latest image:
docker run --name fpst -dit fpst:latest
To test our package, we can use the bash function of the container:
docker exec -it fpst bash
Once inside the container terminal, we can find our plugin package and test it:
cd src/fsleyes-plugin-shimming-toolbox
make install
Altogether:
docker rm --force fpst
docker build --tag fpst:latest .
docker run --name fpst -dit fpst:latest
docker exec -it fpst bash
If you want to test the plugin on arm and you are using an M1/M2 mac, use the following commands:
docker rm --force fpst
docker build --platform linux/amd64 --tag fpst:latest .
docker run --name fpst -dit fpst:latest
docker exec -it fpst bash
To test on different operating systems, you will need to use a virtual machine. You will need to
install VirtualBox: https://www.virtualbox.org/wiki/Downloads. You will also need to install
the Oracle VM VirtualBox Extension Pack in order to test MacOSX.
Vagrant is a tool that interfaces with VirtualBox and streamlines the process:
https://learn.hashicorp.com/tutorials/vagrant/getting-started-index?in=vagrant/getting-started
We have 3 different folders with Vagrantfiles for testing each OS:
| testing
| -- vagrant_linux/
| -- vagrant_mac/
| -- vagrant_windows/
To create the virtual box, run:
cd testing/vagrant_{OS}
vagrant up
Next, ssh into the shell and run the fsleyes-plugin-shimming-toolbox installer:
cd src/fsleyes-plugin/shimming-toolbox/
sudo make install
source /Users/vagrant/.bashrc
To convert the install to an editable developer install:
source /Users/vagrant/shimming_toolbox/python/etc/profile.d/conda.sh
sudo pip3 install -e .
Currently this is only functional for the Mac VirtualBox. When you run vagrant up, a GUI
should open. When you see the login screen, enter:
user: vagrant
password: vagrant
You can open a terminal from this GUI, and run FSLeyes by:
cd src/fsleyes-plugin/shimming-toolbox/
shimming-toolbox
To stop the box from running (but not remove it):
vagrant suspend
To resume the box:
vagrant resume
To remove the box completely:
vagrant destroy
If you update your Vagrantfile and you want to reload the box:
vagrant reload