Google Summer of Code 2022 Weekly Status Reports

We are going to try something new that we introduced in 2020. This is in addition to your blog post. The goal is to catch things early if you are behind in your timeline early.

@gsoc2022contributors:

Answer the following questions in a once-weekly post on Fridays:

  • What progress have you made this week?
  • What do I plan to do next week?
  • Have you had any blockers or issues that are impeding your project?

The point of these is to catch any issues you are having and to handle them early.

Any questions can be directed towards @judywawira, @sunbiz, @downey, or myself.

Note: You aren’t required to do this until 2022-06-17T23:59:00Z and every Friday before 23:59 UTC. There is a short 24hr grace-period.

Please note: The only posts on this topic should be the progress reports. No need to respond to posts, if there is an issue, use the project topics.

Well, I am not sure if we have to post during this week, but I would like to share my progress.

What progress have you made this week?

I have found the required datasets on Kaggle and / or requested access to data from the owners and uploaded it to my Kaggle profile

What do I plan to do next week?
After the meeting with my mentor I will come up with a plan, but for now I will just continue studying papers related to my work

Have you had any blockers or issues that are impeding your project?
The only problem is the large Cholec-80 dataset, which is hard to process, but I guess that using stratified samples for training and a fixed sample for validation is fine

1 Like

What progress have you made this week?
I first finished with the coding pattern and architecture planning a day before coding period started. Then I made the following progress:

  • Created the traditional login flow with username, password and serverURL. There was a slight modification from the ECEB app as the organisation doesn’t have to be manually entered. MR can be seen here.
  • Created local authentication for storing credentials for fast logins so medical professionals working in different organisations don’t waste time in tedious effort of entering things manually all the time. MR can be seen here.
  • Created a basic CI/CD pipeline. MR can be seen here.
  • Setup localization of the app.

What I plan to do next week?
Next week, I plan to implement addition of TEI in the homepage and create a mock peripheral. Then initiate connection between mock BLE and the app.

Have you had any blockers or issues that are impeding your project?

  • @sunbiz I needed some information about initial data needed to be entered while enrolling a baby. I have read up some things in that matter but it will definitely need some improvement.
  • Mock data vitals which were given from the device during testing phase are also required.
    These things will be needed in the subsequent week.
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What progress have you made this week?

I have been learning FHIR and did the setup for HAPI’s FHIR Server and started the React project

  • Forked the repo and removed the angular app and created a React.js project in it with the typescript template.
  • Got a good understanding of the FHIR Standard and wrote this blog
  • Decided on a data fetching architecture using React Query and Axios (the company I am currently interning at uses this, and it is highly scalable)

What progress have you made this week?

Next week:

  • Implement the routes
  • Add the data fetching architecture (which involves caching) to the project
  • Set up the CI and CD pipeline for the project
  • Implement the Patient CRUD using this architecture

Have you had any blockers or issues that are impeding your project?

I had some issues with the HAPI FHIR which are now resolved (was related to JDK version on my machine)

P.S. The work I do is saturated during the end of the week, so Friday updates for this week don’t have the work that I think I can do in a week, so next Friday the work will be more than I do in a 5 day week it will instead be the report of a full 7 day week.

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What progress have you made this week?

  • Developed Basic VR Static Template
  • Developed VR Assets in Blender
  • Added Image Radiography Pipeline in Unity
  • Completed VR platform setup

What I plan to do next week?

  • Design the Vitals Pane with mock data from API (mock)
  • Completed the Chat Window Static Design
  • Added the UI Buttons in Unity Layout

Have you had any blockers or issues that are impeding your project?

  • The oculus SDK had some issues with the new XR interaction toolkit in Unity. Reverting back to the older version solved the issue
1 Like

What progress have you made this week?

  • Read papers on VR in medical imaging.
  • Found out a stable way to “simulate” VR for classification and segmentation task
  • Found an interesting approach to object detection on distorted images
  • Found a thread where a way to distort points by coordinates is discussed. It can be applied to object detection

What do I plan to do next week?

  • Try to use the distortion tool for image segmentation
  • Search for any other papers / data / related work
  • Experiment with distortion bounding boxes

Have you had any blockers or issues that are impeding your project?

  • The main problem is the lack of open-source data. The data is someone’s “know how” or simply not published. I guess that it is easier to find a way to distort points rather than to search for data
2 Likes

Like we discussed, we have requested piglet data from our collaborators at Purdue and will share with you to add to the app as demo/mock data.

@all students - please create separate issues on which you are working or planning to work on. Please submit your MR with reference to the issue. We want you all to learn about working in an open-source environment, as much as we want you to finish the project at hand.

What progress have you made this week?

  • I added Material UI and implemented the Layout with Mobile Responsive Navbar, React Router, and Dynamic Breadcrumbs MR
  • Added a CI CD pipeline for the app, which is deployed on Netlify and has two deployments, Preview and Production
  • Added the React Query + Axios Data Fetching Architecture (Caching works out of the box) MR
  • Implemented the get and search patient using this architecture MR

What progress have you made this week?

Next week’s main focus would be to integrate lh-toolkit-webcomponents into my project anyhow and then finish then Patient CRUD

Next week:

  • Implement the Patient Dashboard UI
  • Add create and update in the Patient Flow
  • Find an FHIR API that supports Radiology and implement Add Radiology Order

Have you had any blockers or issues that are impeding your project?

  • I have been having issues when installing lh-toolkit-webcomponents into my project, I have updated the package.json of this repo in hopes of those issues getting fixed. MR

  • HAPI FHIR’s test API doesn’t support Radiology and it is the next thing that is on my task list (following my GSoC proposal) If I don’t find an API that supports it this week I will move forward with other parts of the project. @sunbiz please do suggest some APIs that support Radiology forum post

What progress have you made this week?

  • Added unit tests for authentication. MR
  • Completed the initial profile page.
  • Tracked Entity Instance Enrollment flow (needs some testing I’m on it).
  • Displaying Tracked Entity attributes for family member user group.
  • Worked with DHIS2 and designed the tracker program and user group allocation.
  • Logout complete

What I plan to do next week?

  • Creating STS visualization components
  • Creating components to display the videos
  • Bookmarking video facility.

Have you had any blockers or issues that are impeding your project?
None

What progress have you made this week?

  • Developed multi class and binary segmentation models.
  • Used the proposed technique to adapt their domain to AR

What do I plan to do next week?

  • Do a comprehensive analysis of results, search for improvements
  • Probably start the classification task

Have you had any blockers or issues that are impeding your project?

  • Adaptation of a binary model was simple, however in case of the multi class one I had to change the pipeline a little. Also, the resulting performance of adapted models is lower that the performance of the original one

What progress have you made this week?

  • Developed Chat Interface
  • Designed the server model for connection between the server and the clients

What do I plan to do next week?

  • Complete the Chat and Implement the Video live streaming Feature
  • Implement the UI buttons for play and pause

Have you had any blockers or issues that are impeding your project?

  • The Client Server Model was initially taking a long time for chat delivery. It turned out to be a network congestion issue.

What progress have you made this week?

  • Completed Chat UI
  • Testing the Chat Interface Server

What do I plan to do next week?

  • Design the Video Playback feature
  • Make the UI Curved in VR

Have you had any blockers or issues that are impeding your project?

  • ScrollView is an issue in VR. I am having difficulties implementing it. Presently looking for alternatives

What progress have you made this week?

  • Improved the multi class segmentation model
  • Created a MR with research notebooks

What do I plan to do next week?

  • Look for one more segmentation dataset (most datasets are with CT scans or X-rays, it is not something we can face with in VR-environment)

Have you had any blockers or issues that are impeding your project?

  • GPU resources on Kaggle are limited, so I had to create one more account for training models

What progress have you made this week?

  • Feature to show information of the enrolled baby to the family member and created an MR for the same.
  • Created components to show video content for training purposes.
  • Created STS data viz component using the readily available flutter library making things simpler.

What I plan to do next week?

  • Testing enrollment feature
  • Using a mock BLE using streams to show data in the app which can be replaced by pig data stream once available.
  • I also plan to finish alert functionalities if time permits.

Have you had any blockers or issues that are impeding the project?

  • Datastore can be used for bookmarking as I have used but better alternative can be found.
1 Like

What progress have you made this week?

  • Finally added and used lh-toolkit-webcomponents
  • Create issue for the UI Re-Write with links to design and linked it to MR
  • Implemented the Patient Dashboard > Demographics using these web components
  • Implemented the Edit Patient flow using these web components, with React Query mutations which has caching hence, re-fetching is extremely fast MR

[[ Preview Deployment ]]

What progress have you made this week?

Next week’s main focus would be to discuss the project’s future with @sunbiz and start with the next thing in the pipeline

Next week:

[[ Will update this section after the meet with sunbiz ]]

Have you had any blockers or issues that are impeding your project?

  • No blockers for this week