README

Code associated with developing a ptychography and phase retrieval algorithm for a senior design project

Contents

• Code to generate mock ptychography data for testing
• Ptychography and phase retrieval algorithm
• Arduino C to control LED matrix
• Interface with camera and arduino

To Do:

• Generate mock data
• develop phase retrieval algorithm
• Control LED matrix
• Add LED matrix control code to repository
• Optimize Phase retrieval
• Interface with camera
• Interface with arduino
• Adapt algorithm to new saving scheme
• Automate color image acquisition (maybe)

Getting Started with Git

Both Atlassian and git have fairly detailed reference materials available, and there are scores of other tutorials around the web. Below is a highly-abridged guide.

All of the commands below can be entered on the windows command line, or in git bash. They can also be used in matlab if preceded by !.

Install git

Go here to learn how to install git on whatever platform you're using.

Update your identity using git config --global user.name "John Doe" and git config --global user.email [email protected]. You may also wish to specify a default editor.

Clone the repository

Run git clone https://[email protected]/robthereticent/ptychography.git to clone this repository into a new directory. (This will create a directory called 'ptychography' with this repository inside.) This URL is shown at the top of the page. See this guide for more info.

Make some Commits

There are four places a file can be: the working directory, the staging area, the local repository, and the remote repository.

When making changes, only the working directory is modified. These changes can then be staged for commit using git add. The status of the staging area can be seen with git status, and the exact changes made can be seen with git diff or git diff --staged.

Once changes have been staged, they can be committed to the local repository with git commit. Be sure to specify a good commit message. Try to make atomic commits as much as possible. It is possible to commit only some changes in a file using git add -p if the changes are unrelated. See the link on atomic commits above for details.

Push the changes

When some changes have been committed, the remote repository should be updated with git push. git push origin master may have to be run the first time to specify which remote (origin) and which branch (master). details

If the remote repository has changed, git push will fail. Use git pull --rebase (not git pull) to update the local repository with changes from the remote. After fixing any conflicts, run git push again as normal.

History and Undoing things

Commit history can be viewed with git log or git log --oneline. Which commits to show can be specified in a number of ways, see here or git help log.

Commits can (should) only be changed in the local repository. Commits that have been pushed to the remote repo should not be changed to avoid conflicts. See How to undo things to learn how to undo things. The difference between reset and revert can be somewhat mysterious. This or this may help de-mystify.

Branches

It is generally good practice to keep unrelated features on different branches to avoid conflicts and allow for parallel feature development. A branch can be created using git branch <branch name>. To switch to a branch use git checkout <branch>. The 'main' or default branch is called master. A list of all branches and the current branch can be seen with git branch. To push a branch's commits to a remote repository, use git push <branch> Right after a branch has been created, git push -u origin <branch> must be used to create a branch in the remote repo, and set the upstream reference. More info here.

Once a branch's feature has been completed, and is ready for publishing, it must be merged into the master branch. This is done by checking out the master branch (or whatever branch the feature should be merged into), and running git merge <branch>. If conflicts are present they must be resolved, and a commit message specified. A new commit will be created on the current branch. Here is some information on resolving conflicts.

Going Further

• MATLAB Integration
• Set up SSH keys
• Learn about branching
• Lots more tools

Command Reference

These commands can be used in the matlab command line by preceding them with !. (e.g. !git diff)

Command	Function
git status	Show the status of the repository
git add <file>	Add <file> to the staging area
git reset HEAD <file>	Remove <file> from the staging area
git diff [--staged]	Show exactly what changes have been made
git commit	Commit changes to the (local!) repository
git rm <file>	Remove a file from repo and working directory
git mv <file> <file_to>	Move or rename a file
git log	Show comit history
git log -n --oneline	Show only last n commits, one line each
git pull --rebase	Fetch new changes from remote repository
git push	Push local commits to remote repository
git branch <branch>	Create a new branch called <branch>
git checkout <branch>	Switch to another branch
git checkout -b <branch>	Create a new branch and switch to it
git merge <branch>	Merge <branch> into the current branch
git push <branch>	Push and update tracking information

See also git help <command> and this cheat sheet.