Get latest slides prior to #20 (#24)

.gitignore

@@ -11,10 +11,6 @@
 
 ## site
 .jekyll-cache/ 
-_site/
+_site/ 
 Gemfile.lock
 
-## Kvasir-SEG dataset
-kvasir-seg.zip
-Kvasir-SEG
-

README.md

@@ -1,7 +1,4 @@
 # :nut_and_bolt: Hacking Real-time AI workflows for Surgery :wrench: 
-![fig](program/figures/team-logo.png)
-
-
 Hackathon hosted by CMIC    
 9-10th November 2023    
 https://cmic-ucl.github.io/CMICHACKS/    
@@ -16,7 +13,7 @@ In this hackathon, instructors aim to engage with participants to bring three le
 
 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.
 
-See slides for a quick introduction: https://scikit-surgery.github.io/cmicHACKS2
+See slides for a quick introduction: https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html
 
 ## :sparkles: Project leaders and organisers 
 Leaders: [Zhehua Mao](https://github.com/ZH-Mao) and [Miguel Xochicale](https://github.com/mxochicale)    
@@ -54,12 +51,9 @@ Registration is free and you can get your tickets [here](https://www.eventbrite.
 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. [google-maps](https://maps.app.goo.gl/XXBmo7E9Zq2CqZ4E6)    
 
 ## :computer: Pre-requisites for participants  
-* Participants require to bring their own computers either with CPU or GPU. Computers with GPU will be ideal to prototype models. However, we will also prepare simple AI workflows in google-colabs that does not require GPUs. 
-* Gmail account to prototype models in google colabs.   
-* 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. 
-See further details here [:link:](program/day-one/README.md#1100--1200--intro-and-preparations-to-hack) 
-
+* 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.

program/day-one/README.md

@@ -3,12 +3,10 @@
 ## 11:00 -12:00 > Intro and preparations to hack
 > Hacking: Intro the full AI pipeline and Setting GitHub repository: clone repo, GitHub workflow to code together and document as you hack
 
-1. Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) (or [here](https://github.com/mxochicale/tools/blob/main/github/SSH.md))  
-1.1 Alternatively you can setup your [Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
+1. Setup your [Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)
 2. Clone repo
 ```
-git clone https://github.com/SciKit-Surgery/cmicHACKS2.git  ##using HTTPS
-git clone [email protected]:SciKit-Surgery/cmicHACKS2.git   ##using password-protected SSH key
+git clone https://github.com/SciKit-Surgery/cmicHACKS2.git 
 ```
 3. Workflow for issue management 
 ```mermaid
@@ -57,12 +55,19 @@ IEEE Access. 2021 Mar 4;9:40496-40510. doi: 10.1109/ACCESS.2021.3063716. PMID: 3
 [google-citations](https://scholar.google.com/scholar?cites=11882550127852592683&as_sdt=2005&sciodt=0,5&hl=en)
 
 
-"Confidently Navigating Software as a Medical Device (SaMD) Product Development"
-June 15, 2023, Josh Cates, Tim Thirion and Andinet Enquobahrie
-https://www.kitware.com/confidently-navigating-software-as-a-medical-device-samd-product-development/ 
+Lee, Ji Young, Jinhoon Jeong, Eun Mi Song, Chunae Ha, Hyo Jeong Lee, Ja Eun Koo, Dong-Hoon Yang, Namkug Kim, and Jeong-Sik Byeon. 
+"Real-time detection of colon polyps during colonoscopy using deep learning: systematic validation with four independent datasets." 
+Scientific reports 10, no. 1 (2020): 8379.
+[google-citations](https://scholar.google.com/scholar?cites=6958241942401260456&as_sdt=2005&sciodt=0,5&hl=en)
 
+Nogueira-Rodríguez, Alba, Rubén Domínguez-Carbajales, Fernando Campos-Tato, Jesus Herrero, Manuel Puga, David Remedios, Laura Rivas et al. 
+"Real-time polyp detection model using convolutional neural networks." 
+Neural Computing and Applications 34, no. 13 (2022): 10375-10396.
+[google-citations](https://scholar.google.com/scholar?cites=10921968363398150924&as_sdt=2005&sciodt=0,5&hl=en)
 
-Labelling tools:   
+
+
+Label tools:   
 * https://www.robots.ox.ac.uk/~vgg/software/via/  
 * https://labelstud.io/  
 * https://github.com/wkentaro/labelme

slides/README.md

@@ -37,7 +37,7 @@ bundle exec jekyll serve
 ```
 2. Open hmtl slides using firefox on a local server.
 ```
-firefox http://127.0.0.1:4000 #or google-chrome http://127.0.0.1:4000
+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
 ```
@@ -48,7 +48,7 @@ rm -rf .jekyll-cache/ _site/ Gemfile.lock
 1. Setting up pages at https://github.com/SciKit-Surgery/cmicHACKS2/settings/pages
 2. Select deploy from a branch, select branch `7-slides` with path `/root` and[SAVE]. Then, you might need to select `main` branch for the final version of the slides.
 3. First GitHub action:  https://github.com/SciKit-Surgery/cmicHACKS2/actions/runs/6747753816
-4. Online slides should be available here https://scikit-surgery.github.io/cmicHACKS2
+4. Online slides should be available here https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html
 
 
 ## References 

slides/figures/agenda/Makefile

@@ -0,0 +1,55 @@
+
+OS_VERSION:=$(shell lsb_release -a 2>/dev/null | grep Description | awk '{ print $$2 "-" $$3 }')
+$(eval $(shell grep VERSION_ID /etc/os-release))
+#ifeq ($(VERSION_ID), 22.04)
+ifeq ($(OS_VERSION), Ubuntu-22.04.1)
+EXPORT_ID = --export-png
+else
+EXPORT_ID = --export-filename
+endif
+# https://stackoverflow.com/questions/714100/os-detecting-makefile
+
+INKSCAPE?=inkscape --export-dpi=200 $(EXPORT_ID)
+
+
+#dPDFSETTINGS=screen #lower quality, smaller size. (72 dpi)
+#dPDFSETTINGS=ebook #for better quality, but slightly larger pdfs. (150 dpi)
+#dPDFSETTINGS=prepress #output similar to Acrobat Distiller "Prepress Optimized" setting (300 dpi)
+#dPDFSETTINGS=printer #selects output similar to the Acrobat Distiller "Print Optimized" setting (300 dpi)
+dPDFSETTINGS=default #selects output intended to be useful across a wide variety of uses, possibly at the expense of a larger output file
+
+GS?=gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/$(dPDFSETTINGS) -dNOPAUSE -dQUIET -dBATCH -sOutputFile=
+
+FIGURES_SVG=$(wildcard vectors/*.svg)
+FIGURES_PNG=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=.png))
+FIGURES_PDF=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=.pdf))
+FIGURES_PDF_REDUCED_SIZE=$(subst vectors/,outputs/,$(FIGURES_SVG:.svg=_reduced_size.pdf))
+
+# Pattern rule for converting SVG to PNG and PDF
+png:	$(FIGURES_PNG)
+outputs/%.png: vectors/%.svg
+	$(INKSCAPE) $(@) $(<)
+
+pdf:	$(FIGURES_PDF)
+outputs/%.pdf: vectors/%.svg
+	$(INKSCAPE) $(@) $(<)
+
+edit:
+	inkscape $(FIGURES_SVG)
+
+view-png:
+	eog $(FIGURES_PNG)
+
+view-pdf:
+	evince $(FIGURES_PDF)
+
+reduce-pdf-size:
+	$(GS)$(FIGURES_PDF_REDUCED_SIZE) $(FIGURES_PDF)
+
+clean:  ##  output figure files
+	rm -f $(FIGURES_PNG) $(FIGURES_PDF) outputs/*.pdf
+
+test:
+	echo $(VERSION_ID)
+	echo $(OS_VERSION)
+	echo $(EXPORT_ID)

slides/figures/agenda/README.md

@@ -0,0 +1,44 @@
+# Vector figures
+
+## Notes
+
+## Usage 
+```
+make png
+make pdf
+make view-png #eog *.png
+make view-pdf #evince *.pdf
+make reduce-pdf-size dPDFSETTING=book # screen, ebook, prepress, printer and default
+make edit # inkscape vector/drawing-v$NN.svg
+make clean
+```
+
+## tree file and file size
+```
+tree -s
+[       4096]  .
+├── [       1771]  Makefile
+├── [       4096]  outputs
+│   ├── [       8378]  drawing-v00.pdf
+│   ├── [      30203]  drawing-v00.png
+│   ├── [       9015]  drawing-v00_reduced_size.pdf
+│   └── [         70]  README.md
+├── [        508]  README.md
+├── [       4096]  references
+│   └── [         15]  README.md
+└── [       4096]  vectors
+    └── [       6982]  drawing-v00.svg
+
+3 directories, 8 files
+
+```
+
+## Download template
+Open a terminal and type:
+```
+cd ~/Desktop &&svn checkout https://github.com/mxochicale/figures/trunk/00_template-vector-images
+cd 00_template-vector-images && rm -rf .svn
+```
+
+# References
+https://stackoverflow.com/questions/7106012/download-a-single-folder-or-directory-from-a-github-repo

slides/figures/agenda/outputs/README.md

@@ -0,0 +1,6 @@
+# Versions
+## v01
+![v](drawing-v01.png)
+
+## v00
+![v](drawing-v00.png)

slides/figures/agenda/references/README.md

@@ -0,0 +1,3 @@
+# References
+
+