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Activities completed this month
  1. I finished re-writing the transcript for Carolyn.
  2. Reminded Jayashree to send invoices for Sept (new contract).
  3. Finished UI development and api construction of docker image upload.
  4. Received scoring program for SPIE-AAPM Breast Cancer Challenge. Added to challenge site.
  5. Updated SPIE-AAPM site to include new validation phase data.
  6. Get PIV card for NIH access (appointment is scheduled for 12/22/2020). UPDATE: Done
  7. Kevin Olexa, from NCI is tried upgrading the JQuery of their deployment of the codalab MedICI instance over at NCI/NIH. It seems it will be a lot of work. The new plan is to have me try out the v2 codalab otherwise known as codabench (https://www.codabench.org/). This was built with python3 and jQuery 3+. This should circumvent any issues with up to date packages.
Planned for next month
  1. The SPIE-AAPM Breast Cancer challenge has started (25 participants). Challenge link: http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/. Will need to double check that they have the scoring program ready.
  2. Updated SPIE-AAPM site to include new validation phase data.
  3. Added support link and message regarding using the api for image and metadata downloads.
  4. Investigated Kheops and am finishing the report.
Planned for next month
  1. (I know it is not right now..).Add Okta as supported feature in MedICI GitHub and website.
  2. Wrap up the SPIE-AAPM Breast Challenge and collect final scores for the challenge organizers. 
  3. Continue ascertaining the validity of v2 codalab (codabench)
  4. Add support link and message regarding using the api for image and metadata downloads.
  5. Finish creating the MedNIST sample challenge on COVID-Kubernetes deployment and address some bugs listed below:
    1. In results table the "FILENAME" is always "trackingid", needs to be the image that was submitted.
    2. Image Uploads are slow and we need to address that. 
    3. Sometimes deleting an image from the repo changes the image upload html and I have to reset it. This shouldn't happen.
  6. Setup DL-sparse-view CT Grand Challenge (I'm a little behind on this)
Comments

Things that went well:

SPIE-AAPM Challenge for reference:

http://spie-aapm-nci-dair.westus2.cloudapp.azure.com/


  • I have Patrick's code loaded and working almost in the cloud. While extremely close, the COVID challenge this was being built for will need to proceed with plan b. This is the standard docker submission we have talked about and will also have Okta integration and docker upload functionality. We won't need to go with plan-b anymore as it seems the kubernetes cluster deployment is working well.
  • Scoring program integration for SPIE-AAPM was seamless. Mateusz Buda, a data scientist working on the Breast challenge, created an easy to use evaluation script that I could tie into codalab and is being used to score submissions.
  • I have the start of the codabench deployed and it almost works. There is a problem with the static files not being able to be found so there is no style on the web app when browsed to.
  • The forum and issue tracker were used in the SPIE-AAPM challenge



Things that could be improved:

  • SPIE challenge test phase leader board was showing multiple submissions by participants and should only show their best score. I can and did fix it manually but it's not ideal.
MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

Milestones

DescriptionDate
  • UI for uploading docker images is created.

 

  • COVID challenge plan-a is up and working

 

Task

DescriptionResolutionStatusCreation DateClose Date

...

DescriptionMitigationRankStatusCreation DateRealizationClose Date
Ingress service in Kubernetes is not behaving like the standard tutorials or documentationKeep plugging away to find the correct configuration1closed

 

Azure has inconsistent docs on how to set this service up.

01 - 06 - 2021: Patrick's new changes worked out the kink.

 

Challenge taking too long to setup. People are worried about it failing to materialize

We really need a solid deployment of this architecture on Azure. Basic functionality is not working and some of the harder stuff is still being developed.

1

Open

 

Now that CodaLab has been deconstructed from its normal configuration (postgres as an azure service rather than container; codalab as a pod in kubernetes instead of container; codalab code in azure file shares rather than the host machine), getting all the pieces to talk to one another isn’t working seamlessly yet.

01 - 06 - 2021: Plan b is in full swing


 

Scoring program not ready for the SPIE-AAPM challengeI have drafted a preliminary white board thought process to understand the desired implementation. I have a couple questions, but could turn it into code if I had to. 2OpenClosed

 

Scoring program works and is in place for Breast challenge.