F-image

F-image is a package management system used to install and manage software packages written for functional image analysis.

why F-image?

There are many independently developed toolboxes for processing functional imaging data. F-image can automatically install and load the selected packages for specific tasks. It makes reusing functions between packages easier.

Example

fi.install('cnmfe');   # install CNMF-E 
fi.usepkg('cnmfe');    # use CNMF-E functions in your code.

Goals

simplify the steps of installing and using packages of functional image analysis (mainly calcium/voltage imaging for now).
community curated list of functional imaging analysis toolboxes.
standardize data communications between packages. A customized pipeline for processing data contains multiple steps, and we use F-image to ensure seamless communications.
share customized pipelines for processing one type of data. You can just tell what packages to be included and F-image will handle the rest.
reduce the effort of developing your packages by reusing other packages. All you need to do for calling functions in other packages is
```
fi.install(pkg_name); 
fi.usepkg(pkg_name); 
```

Installation

Open MATLAB and set the current working directly to the place you want to install F-image, then run the following command

try
    system('git clone https://github.com/zhoupc/F-image.git'); % with git
catch
    unzip('https://github.com/zhoupc/F-image/archive/master.zip');  % not git installed
    movefile('F-image-master', 'F-image')
end
cd F-image;
fimage_setup;

How to use

Here we use CNMF-E as an example to show how F-image manages packages.

>> pkg_name = 'cnmfe';

list all supported packages (currently supported packages)
```
>> fi.list_supported(); 
```
install a package
```
>> fi.install(pkg_name); 
```
use a package
```
>> fi.usepkg(pkg_name); 
```
remove a package
```
>> fi.remove(pkg_name);
```
update a package
```
>> fi.update(pkg_name);
```
get the package path
```
>> pkg_path = fi.locate(pkg_name); 
```
show package information
```
>> json_path = fi.pkginfo(pkg_name); 
```
add a new package info
```
>> fi.add_pkginfo(pkg_name); 
```

fix errors in the package info

>> fi.fix_pkginfo(pkg_name, only_fix_missing_values); % only_fix_missing_vlaues (default: true) is a boolean value

list all installed packages
```
>> fi.list_installed(); 
```
show the path of F-image
```
>> fi.home_dir(); 
```
push changes to the github repo
```
>> fi.push_github(); 
```
update F-image
```
>> fi.selfupdate(); 
```

Add a new package

You need two steps to add a package to F-image

create a json file pkgname_matlab.json (see template.json) and save it to the folder F-image/pkgname/pkginfo. You can also provide these info in the command window,
```
>> fi.add_pkginfo(pkg_name); 
```
Here are some example json files.

The package won't be installed until you run
```
>> fi.install(pkg_name) 
```
configure the way of using the package, which usually simply add the package path to the MATLAB searching paths (default option). If you need some special configurations, modify the file +fi/usepkg.m, where you can find example configurations.
```
>> edit fi.usepkg   
```

Copyright

Pengcheng Zhou @Columbia University, 2019

zhoupc / F-image