adds local working slides.hmtl with libs #7

SciKit-Surgery · Nov 3, 2023 · a2e960d · a2e960d
1 parent 8deb60d
commit a2e960d
Show file tree

Hide file tree

Showing 99 changed files with 10,641 additions and 292 deletions.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
diff --git a/.github/ISSUE_TEMPLATE/not_working.md b/.github/ISSUE_TEMPLATE/not_working.md
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,8 @@
 ## ignores temporal files
 **/*.swp
 
+## site
+.jekyll-cache/ 
+_site/ 
+Gemfile.lock
+
diff --git a/Gemfile b/Gemfile
@@ -0,0 +1,2 @@
+source "https://rubygems.org"
+gem "jekyll"
diff --git a/README.md b/README.md
@@ -1,60 +1,59 @@
-# :nut_and_bolt: Hacking Real-time AI workflows for Surgery :wrench: 
-Hackathon hosted by CMIC    
-9-10th November 2023    
-https://cmic-ucl.github.io/CMICHACKS/    
-
-## :scroll: Project description
-Artificial Intelligence (AI)-based surgical workflows use input from multiple sources of data (e.g., medical devices, trackers, robots, cameras, etc) with different Machine Learning and Deep Learning tasks (e.g., classification, segmentation, synthesis, etc) and have been applied across different surgical and acquisition workflows.
-However, the diversity of data sources, pre-processing methods, training and inference methods make a challenging scenario for low-latency applications in surgery.
-In this hackathon, instructors aim to engage with participants to bring three learning outcomes:
-* participants will learn to train, optimise, test and deploy AI models for detection and tool tracking, 
-* participants will learn good software practices to contribute to our open-source projects aligning with medical device software standard (IEC 62304), and 
-* participants will have the chance to work with NVIDIA Clara AGX - A Universal computing architecture for next-generation AI medical instruments.    
-
-We hope to bring together researchers, engineers and clinicians across different departments to hack workflows for real-time AI for Surgery (development, evaluation and integration) and hopefully to sparking future collaborations.
-
-
-## :sparkles: Project leaders and organisers 
-Leaders: [Zhehua Mao](https://github.com/ZH-Mao) and [Miguel Xochicale](https://github.com/mxochicale)    
-Co-organisers: Steve Thompson, Tom Dowrick, Sophia Bano, Matt Clarkson at UCL; and Mikael Brudfors at NVIDIA
-
-## :date: Agenda
-The following is a general agenda that might have slightly changes.
-
-### Thursday 9th Nov 2023 
-| Time  | Activity                                                            |
-| --- |---------------------------------------------------------------------|
-| 9:00 – 10:00 | Setting up                                                          |
-| 10:00 – 11:00 | Welcome session                                                     |
-| 11:00 -12:00 | Hacking: Intro and preparation to hack [:link:](program/day-one/README.md#1100--1200--intro-and-preparations-to-hack)                   |
-| 12:00 - 13:00 | Lunch                                                               | 
-| 13:00 - 15:00 | Hacking: Get familiar with your data [:link:](program/day-one/README.md#1300---1500--get-familiar-with-your-data) |
-| 15:00 - 15:15 | Coffee break                                                        | 
-| 15:15 - 17:00 | Hacking: Training AI workflow [:link:](program/day-one/README.md#1515---1700--hacking-training-ai-workflow)                                      | 
-| 17:00 – all night | Social                                                              |
-
-### Friday 10th Nov 2023 
-| Time  | Activity                                                                        |
-| --- |---------------------------------------------------------------------------------|
-| 09:00 - 10:30 | Hacking: Evaluation of AI models with benchmarks [:link:](program/day-two/README.md) |
-| 10:30 - 10:45 | Coffee break                                                                    | 
-| 10:45 - 12:00 | Hacking: Optmise, test and deploy AI models in clara-agx [:link:](program/day-two/README.md)                       |
-| 12:00 - 13:00 | Lunch                                                                           |
-| 13:00 - 14:30 | Hacking: Deploying models to nvidia-clara-agx [w/Mikael Brudfors] [:link:](program/day-two/README.md)              | 
-| 14:30 – 14:45 | Coffee break                                                                    |
-| 14:45 - 16:30 | Hacking: Tidied up documentation and present results [w/Mikael Brudfors]  [:link:](program/day-two/README.md)      | 
-| 16:30 - 17:00 | Closing session                                                                 |
-
-## :school: Registration and venue
-Registration is free and you can get your tickets [here](https://www.eventbrite.co.uk/e/cmichacks-2-tickets-733294452447)
-The venue of the hackathon is Jeffery (Thursday) and Elvin (Friday) rooms, Level 1, main UCL Institute of Education (IOE) building, 20 Bedford Way, London WC1H 0AL.    
-
-## :computer: Pre-requisites for participants  
-* Participants require to bring their own computers either with CPU or GPU. Computers with GPU will be idea to prototype models. However, we will also prepare pre-training models and simple AI workflows that does not require GPUs. 
-* Have a Github username. Otherwise, [sign up](https://docs.github.com/en/get-started/signing-up-for-github/signing-up-for-a-new-github-account) to GitHub to create an account.
-* Clone https://github.com/SciKit-Surgery/cmicHACKS2.git  
-
-## :family: Forum
-We are using [Discussions](https://github.com/SciKit-Surgery/cmicHACKS2/discussions/) as a place to connect with other members of our community.
-Ask questions you’re wondering about, share ideas, engage with other community members, welcome others and are open-minded. 
-Remember that this is a community we build together 💪!
+# Slides :nut_and_bolt: Hacking Real-time AI workflows for Surgery :wrench: 
+
+## 💻 Machine and OS
+```
+$ hostnamectl
+
+ Static hostname: --
+       Icon name: computer-laptop
+         Chassis: laptop
+      Machine ID: --
+         Boot ID: --
+Operating System: Ubuntu 22.04.1 LTS              
+          Kernel: Linux 5.15.0-56-generic
+    Architecture: x86-64
+ Hardware Vendor: --
+
+```
+
+## 💾 Requirements and dependencies for GNU/Linux
+```
+sudo apt-get install ruby-full build-essential zlib1g-dev
+echo '# Install Ruby Gems to ~/gems' >> ~/.bashrc
+echo 'export GEM_HOME="$HOME/gems"' >> ~/.bashrc
+echo 'export PATH="$HOME/gems/bin:$PATH"' >> ~/.bashrc
+source ~/.bashrc
+gem install jekyll bundler
+```
+For others OSs, see https://jekyllrb.com/docs/installation/
+
+
+## 💻 Local testing of html slides
+
+Open two terminals: 
+1. to build the site:     
+```
+bundle exec jekyll serve
+```
+2. Open hmtl slides using firefox on a local server.
+```
+firefox http://127.0.0.1:4000/slides.html #or google-chrome http://127.0.0.1:4000/slides.html
+```
+3. You might like to remove build files
+```
+rm -rf .jekyll-cache/ _site/ Gemfile.lock
+```
+
+## 🎒 Steps to create github pages 
+1. Setting up pages at https://github.com/SciKit-Surgery/cmicHACKS2/settings/pages
+2. During development, select `branch` with path `/root` and[SAVE]. Then, you might need to select `main` branch for the final version of the slides.
+3. Github action:  
+4. Online slides should be available here    /slides.html
+
+## References 
+* https://github.com/oss-for-surgtech/ucl-open-science-awards-2023/tree/main/slides 
+* https://github.com/mxochicale/tools/tree/main/html-slides  
+* ONLINE-HTML-SLIDES: https://mxochicale.github.io/tools/html-slides/template/slides.html  
+* HMTL-SOURCE: https://github.com/mxochicale/tools/blob/main/html-slides/template/slides.html  
+* https://github.com/hakimel/reveal.js/tree/master/dist/theme 
+