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Added a yml file to build the docker image #74

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Merged
merged 19 commits into from
Oct 28, 2024
Merged

Added a yml file to build the docker image #74

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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
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48 changes: 48 additions & 0 deletions .github/workflows/docker-build-and-run.yml
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name: Build and Run Docker

on:
push:
branches:
- main
pull_request:
types: [opened, synchronize, edited]
branches:
- main
- "docker/**"

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

- name: Build Docker image
run: |
docker build -t tf2.4_ivim-mri_codecollection -f Docker/Dockerfile .

- name: Save Docker image to a tarball
run: |
docker save -o tf2.4_ivim-mri_codecollection.tar tf2.4_ivim-mri_codecollection
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These things are large, how about also zipping it.


- name: Upload Docker image artifact
uses: actions/upload-artifact@v4
with:
name: docker-image
path: tf2.4_ivim-mri_codecollection.tar

- name: Run Docker container
run: |
docker run --rm --name TF2.4_IVIM-MRI_CodeCollection \
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We should confirm that images are actually generated. Maybe not the exact values in the images, but even that the files we expect exist.

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Yeah, exactly.

-v ${{ github.workspace }}:/usr/src/app \
-v ${{ github.workspace }}:/usr/app/output \
tf2.4_ivim-mri_codecollection brain.nii.gz brain.bvec brain.bval
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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.

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How to go about the reading the small text file ?

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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.


- name: Clean up
run: |
docker rmi tf2.4_ivim-mri_codecollection
rm tf2.4_ivim-mri_codecollection.tar
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