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Merge pull request #5 from HealthBioscienceIDEAS/4-excercise4
4 - Exercise 4 with itk-snap
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‎.gitignore‎

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## vim temp files
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*.swp
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## .nii.gz
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*.nii.gz
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# sandpaper files
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episodes/*html
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site/*
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# renv sandbox needed for renv version 0.16.0
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renv/sandbox # OPTIONAL
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‎CONTRIBUTING.md‎

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### Using GitHub
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If you choose to contribute via GitHub, you may want to look at [How to
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Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we
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use [GitHub flow][github-flow] to manage changes:
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1. Create a new branch in your desktop copy of this repository for each
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significant change.
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2. Commit the change in that branch.
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3. Push that branch to your fork of this repository on GitHub.
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4. Submit a pull request from that branch to the [upstream repository][repo].
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5. If you receive feedback, make changes on your desktop and push to your
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branch on GitHub: the pull request will update automatically.
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#### Committing and pushing changes
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1. Clone this repo
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```
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git clone git@github.com:UCL/real-time-ai-for-surgery.git
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```
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2. Create new branch using issue number
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```
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git checkout -b ISSUENUMBER-branch-name
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```
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3. Commit changes and push to your branch
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```
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git add .
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git commit -m 'short message (#ISSUENUMBER)'
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git push origin ISSUENUMBER-branch-name
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```
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4. Submit a Pull Request against the `main` branch.
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#### Pull Request (PR) and merge to `main` branch
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1. Select branch that contain your commits.
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2. Click `Compare and pull request` and create PR for the associated branch.
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3. Type a title and description of your PR and create PR
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4. Please keep your PR in sync with the base branch.
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```
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git checkout main
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git pull origin main
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git checkout FEATURE_BRANCH
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git rebase main
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git push --force origin FEATURE_BRANCH
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```
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4.1 In case you are in a different `MY_FEATURE_BRANCH` branch, follow:
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```
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git checkout FEATURE_BRANCH
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git pull origin FEATURE_BRANCH
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git checkout MY_FEATURE_BRANCH
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git rebase FEATURE_BRANCH
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git push --force origin MY_FEATURE_BRANCH
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```
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5. Run `pre-commit` to tidy up code and documentation (see next section).
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6. Request a PR review.
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See [collaborating-with-pull-requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests) for further details.
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7. Once your PRs has been approved, procced to merge it to main. See [Merging a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/merging-a-pull-request)
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8. Remove your merged branch from your repo and in the list of https://github.com/UCL/real-time-ai-for-surgery/branches
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```
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#Local git clear
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git branch --merged | grep -v '\*\|master\|main\|develop' | xargs -n 1 git branch -d
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#Remote git clear
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git branch -r --merged | grep -v '\*\|master\|main\|develop' | sed 's/origin\///' | xargs -n 1 git push --delete origin
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```
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NB: The published copy of the lesson is usually in the `main` branch.
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‎README.md‎

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## Medical-Image-Registration-Short-Course
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This is the lesson repository for Medical-Image-Registration-Short-Course
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This is the lesson repository for [Medical-Image-Registration-Short-Course](https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course)
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## Setting up and preview sandpaper
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See [details](_setting_up) to setup sandpaper and its dependencies. Otherwise you are ready to preview your work:
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```
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R
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sandpaper::build_lesson()
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```
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‎_dependencies/README.md‎

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# Dependencies
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* Using conda
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```
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conda create -n "mirVE" python=3.11 pip -c conda-forge
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conda activate mirVE
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cd /_dependencies
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pip install -r requirements.txt
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conda list -n mirVE #to check installed packages
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conda remove -n mirVE --all #in case you want to remove it
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```
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* Using python virtual environment
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```
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# Installing dependencies in Ubuntu 22.04
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sudo apt-get install -y python3-pip
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sudo apt-get install -y python3-venv
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# Create path for venv
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cd $HOME
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mkdir mirVE
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cd mirVE
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# Create virtual environment
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python3 -m venv mirVE
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source mirVE/bin/activate
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cd /_dependencies
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python3 -m pip install -r requirements.txt
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```

‎_dependencies/requirements.txt‎

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numpy
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matplotlib
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dicom2nifti
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nibabel

‎_setting_up/README.md‎

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# INSTRUCTIONS for installing R, Carpentries, and previewing Sandpaper for multi OS (Linux, Windows and Mac)
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## Steps in Ubuntu 22.04 x64
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1. Create new repo: https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course
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2. Clone repo `git clone https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course`
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3. install R (if you haven't done already) [:link:](https://cran.r-project.org/bin/linux/ubuntu/)
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```
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sudo apt-get install r-cran-xml
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sudo apt-get install libxml2-dev
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sudo apt install libgit2-dev
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sudo apt install r-cran-curl
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```
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4. Open R and run the following to install dependencies
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```
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages(c("remotes"), dep =TRUE)
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```
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5. In R, run
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```
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remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)
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# this one is taking some 20mins the fist time as it seems is building various packages
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# Terminal logs
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Downloading GitHub repo HealthBioscienceIDEAS/sandpaper@HEAD
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These packages have more recent versions available.
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It is recommended to update all of them.
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Which would you like to update?
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1: All
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2: CRAN packages only
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3: None
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4: pegboard (0.7.5 -> a32a7836d...) [GitHub]
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5: varnish (1.0.2 -> 56d594d27...) [GitHub]
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6: curl (4.3.2 -> 5.2.1 ) [CRAN]
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7: httr (1.4.2 -> 1.4.7 ) [CRAN]
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8: gh (1.3.0 -> 1.4.1 ) [CRAN]
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9: covr (3.5.1 -> 3.6.4 ) [CRAN]
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Enter one or more numbers, or an empty line to skip updates: 1
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The downloaded source packages are in
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‘/tmp/Rtmpn94NAu/downloaded_packages’
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Downloading GitHub repo carpentries/pegboard@HEAD
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These packages have more recent versions available.
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It is recommended to update all of them.
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Which would you like to update?
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1: All
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2: CRAN packages only
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3: None
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4: tinkr (0.2.0.9000 -> be564d524...) [GitHub]
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Enter one or more numbers, or an empty line to skip updates: 1
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── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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✔ checking for file ‘/tmp/Rtmpn94NAu/remotes50ddb31b7ca85/HealthBioscienceIDEAS-sandpaper-fb14e02/DESCRIPTION’ ...
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─ preparing ‘sandpaper’:
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✔ checking DESCRIPTION meta-information ...
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─ checking for LF line-endings in source and make files and shell scripts (420ms)
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─ checking for empty or unneeded directories
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Omitted ‘LazyData’ from DESCRIPTION
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─ building ‘sandpaper_0.16.4.tar.gz’
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Installing package into ‘/home/mxochicale/R/x86_64-pc-linux-gnu-library/4.4’
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(as ‘lib’ is unspecified)
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* installing *source* package ‘sandpaper’ ...
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** using staged installation
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** R
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** inst
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** byte-compile and prepare package for lazy loading
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** help
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*** installing help indices
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*** copying figures
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** building package indices
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** installing vignettes
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** testing if installed package can be loaded from temporary location
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** testing if installed package can be loaded from final location
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** testing if installed package keeps a record of temporary installation path
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* DONE (sandpaper)
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Warning message:
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In i.p(...) : installation of package ‘curl’ had non-zero exit status
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```
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6. In R, run
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```
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sandpaper::create_lesson("~/Desktop/medical-registration/Medical-Image-Registration-Short-Course")
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## LOGS
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> sandpaper::create_lesson("~/Desktop/medical-registration/Medical-Image-Registration-Short-Course")
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No personal access token (PAT) available.gistration/Medical-Image-Registration-Short-Course...
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Obtain a PAT from here:
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https://github.com/settings/tokens
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For more on what to do with the PAT, see ?gh_whoami.
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ℹ No schedule set, using Rmd files in episodes/ directory.
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→ To remove this message, define your schedule in config.yaml or use `set_episodes()` to generate it.
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───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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ℹ To save this configuration, use
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set_episodes(path = path, order = ep, write = TRUE)
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• Edit '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/episodes/introduction.Rmd'
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✔ First episode created in /home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/episodes/introduction.Rmd
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ℹ Workflows up-to-date!
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✔ Lesson successfully created in ~/Desktop/medical-registration/Medical-Image-Registration-Short-Course
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✔ Setting active project to '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course'
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✔ Changing working directory to '/home/mxochicale/Desktop/medical-registration/Medical-Image-Registration-Short-Course/'
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~/Desktop/medical-registration/Medical-Image-Registration-Short-Course
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>
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```
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7. Setting up config file in sandpaper template:
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```
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carpentry: 'IDEAS'
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title: ''Medical-Image-Registration-Short-Course'
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created: '2024-05-13'
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source: 'https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course'
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varnish: 'HealthBioscienceIDEAS/varnish@IDEAS'
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sandpaper: 'HealthBioscienceIDEAS/sandpaper@IDEAS'
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```
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8. Set up GitHub Pages
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* Go go [pages](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/settings/pages) and select gh-pages branch with `/root` and click save
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* Pass CI [actions](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/actions/runs/9064118161)
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* :tada: you have created: https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course/
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## Steps on Windows
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### **INSTRUCTIONS for installing R, Carpentries, and Sandpaper on Windows:**
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1. Create new repo: https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course
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2. Clone repo `git clone https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course`
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3. Installing R using the following: https://cran.r-project.org/bin/windows/base/
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4. Using the default settings during the installation of **RGUi 4.x.x**
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5. From RGui Console, enter the following command:
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```
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options(repos = c(
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carpentries = "https://carpentries.r-universe.dev/",
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CRAN = "https://cran.rstudio.com/"
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))
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install.packages(c("remotes"), dep =TRUE)
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```
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6. Enter the following command:
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`remotes::install_github("HealthBioscienceIDEAS/sandpaper", dependencies = TRUE)
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`
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7. Change path from RGUi to the GitHub folder of the medical image registration course. This is done from the Menu list by picking 'File' then 'Change Dir..'
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8. Run the following command to start sandpaper:
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`sandpaper::build_lesson()
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`
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9. You may notice some package not installed called _**Pandoc**_ after running the sandpaper command. If so, install Pandoc then run _step 8_ again.
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Pandoc installation: https://pandoc.org/installing.html
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## Steps in MAC
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Packages via homebrew: freetype, fribidi, harfbuzz, libpng, git2.
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## Previewing eposides in any OS platform
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1. Using your terminal clone repo
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```
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git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git
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```
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2. Checkout `feature-branch-name`.
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```
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git checkout feature-branch-name
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```
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3. Run `sandpaper::build_lesson()` in R which will launch your internet browser with the episode
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```
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R
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sandpaper::build_lesson()
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```
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‎config.yaml‎

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# Order of episodes in your lesson
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episodes:
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- introduction.Rmd
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#- introduction.Rmd
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- itksnap.Rmd
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- excthreesteps.Rmd
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# Information for Learners
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learners:

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