Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added a yml file to build the docker image #74

Merged
merged 19 commits into from
Oct 28, 2024
Merged

Added a yml file to build the docker image #74

Changes from 1 commit
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
af49849
Added a yml file to build the docker image
Unique-Usman Aug 11, 2024
c2149da
Removed -it, and also save the docker image as an artifcat
Unique-Usman Aug 13, 2024
863e7f7
Added sample data for running the docker image, also added the script…
Unique-Usman Sep 26, 2024
1fa952c
Fixed the float not subscriptable error
Unique-Usman Sep 26, 2024
7294bde
Generated the testing images during docker building and added confirm…
Unique-Usman Sep 26, 2024
80c1663
Removed erroneus file
Unique-Usman Sep 26, 2024
602f17d
Improve the github actions to install all the required library for ru…
Unique-Usman Sep 26, 2024
33acf99
Added nibabel to the requirement
Unique-Usman Sep 26, 2024
dc9265d
Added debugging output options to the github action
Unique-Usman Sep 26, 2024
7b2f0b8
Added debugging output options to the github action
Unique-Usman Sep 26, 2024
ee2eb99
Change the name of the ivim_image.nii.gz to ivim_simulation.nii.gz
Unique-Usman Sep 26, 2024
a4136f8
used docker buildx for save the docker image as tar file and also mov…
Unique-Usman Oct 1, 2024
a6ddfb2
Revert from archiving to saving then archiving
Unique-Usman Oct 1, 2024
ea69e18
Added Docker cleanup
Unique-Usman Oct 21, 2024
428095e
Change the base image to alpine linux
Unique-Usman Oct 21, 2024
6fee6ed
Change the version of libssl to 3
Unique-Usman Oct 21, 2024
1f6da96
Remove pushing of the image and used slim instead of alpine
Unique-Usman Oct 21, 2024
17b98f8
Merge branch 'main' into main
Unique-Usman Oct 21, 2024
12ae83f
Avoid uploading the docker image
Unique-Usman Oct 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 33 additions & 0 deletions .github/workflows/docker-build-and-run.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
name: Build and Run Docker

on:
push:
branches:
- main
pull_request:
Unique-Usman marked this conversation as resolved.
Show resolved Hide resolved
branches:
- main

jobs:
build-and-run-docker:
runs-on: ubuntu-latest

steps:
- name: Checkout code
uses: actions/checkout@v4

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3

# Build the Docker image
- name: Build Docker image
Unique-Usman marked this conversation as resolved.
Show resolved Hide resolved
run: |
docker build -t tf2.4_ivim-mri_codecollection -f Docker/Dockerfile .
Unique-Usman marked this conversation as resolved.
Show resolved Hide resolved

# Run the Docker container
- name: Run Docker container
run: |
docker run -it --rm --name TF2.4_IVIM-MRI_CodeCollection \
Unique-Usman marked this conversation as resolved.
Show resolved Hide resolved
-v ${{ github.workspace }}:/usr/src/app \
-v ${{ github.workspace }}:/usr/app/output \
tf2.4_ivim-mri_codecollection brain.nii.gz brain.bvec brain.bval
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I don't think the data are available. We could pull it, but that run would take a while. Maybe we could read a small text file that does just a few fits and takes just a second or two. We really just want to run it to confirm it works, we have other tests to check the actual results.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

How to go about the reading the small text file ?

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Perhaps even easier to simulate something. You can generate signals using from utilities.data_simulation.GenerateData import GenerateData. It's done in test_ivim_synthetic.py for example. Then save it to a nifti using the function you wrote, then read the nifti. Maybe just a 10x10x1 or something small and fast. B-values of [0, 50, 100, 200, 500, 1000] with maybe one or two vectors.

Loading