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Activities completed this month
  1. Added Okta as supported feature in MedICI GitHub and website (About Page: https://www.
  • Add support link and message regarding using the api for image and metadata downloads.
  • Investigated Kheops and am finishing the report.
    • Planned for next month
  • Add Okta as supported feature in MedICI GitHub and website.
    1. medici-challenges.org/about).
    2. Added DL Sparse View CT Challenge to MedICI website (About Page: https://www.medici-challenges.org/about).
    3. Launched the DL Sparse view challenge: http://dl-sparse-view-ct-challenge.eastus.cloudapp.azure.com/
    4. Wrapped
    Wraped
    1. up the SPIE-AAPM Breast Challenge and collect final scores for the challenge organizers. 
    Continued ascertaining the validity of v2 codalab (codabench). I honestly haven't had too much time because of the covid challenge platform
    1. Add support link and message regarding using the api for image and metadata downloads.
    2. Got a version of codabench to launch locally on my laptop. Codabench is the new and improved codalab. I still need to launch the miccai challenge on it to test it out.
    3. Investigated Kheops and am finishing the report.
    4. Finished creating the MedNIST sample challenge on COVID-Kubernetes deployment and addressed some bugs listed below:
      1. FIXED: In results table the "FILENAME" is always "trackingid", needs to be the image that was submitted.
        Image Added
      2. FIXED: Image Uploads are slow and we need to address that. The solution we chose was to upload instructions for building an image and have it built on our server and then push it. Before we were sending 6+GB over HTTP. That was slow. Now we only send a couple MB and then we can build the image and send at much faster speeds. 
        Image Added
      3. NOT FIXED: Sometimes deleting an image from the repo changes the image upload html and I have to reset it. This shouldn't happen. This is quite elusive and I haven't spent a ton of time on it. It's really east to reset so it should never fully break the platform, but I do need to reset it every once in a while. I imagine this will become annoying over time and especially weekends.
    5. Setup DL-sparse-view CT Grand Challenge
    (I'm a little behind on this)Comments

    Things that went well:

    SPIE-AAPM Challenge for reference:

    1. :
      UPDATE: I have a site setup: http://
    spie
    1. dl-sparse-
    aapm
    1. view-
    nci
    1. ct-
    dair
    1. challenge.
    westus2
    1. eastus.cloudapp.azure.com/
      Image Added
      TO DO: Upload scoring program and figure out data hosting situation. 
    Planned for next month


    1. Continued ascertaining the validity of v2 codalab (codabench). I honestly haven't had too much time because of the covid challenge platform. I did get it to launch but there are some issues. I plan to get it all ready and deployed with the MICCAI challenge from last year. Once I have that we can scan it on the NCI platform and run challenges there. Deploy "develop" branch of codabench code to see if it is farther along and more bug free.Image Added
    2. Kheops report finalized and request meeting with developers. 
    3. Investigate getting VPN via: https://service.cancer.gov/ncisp
    Comments

    Things that went well:

  • 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
    07 Jan

     

    Bi-weekly Meeting #2
    21 Jan

    Milestones

    DescriptionDate
    • UI for uploading docker images is created.Fixed Image Upload Problem

     

    • COVID challenge plan-a is up and working

     

    ...

    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

    Openclosed

     

    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


    06  

    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. 2Closed

     

    		Scoring program works and is in place for Breast challenge.