rust_abf

Rust ABF Reader

This is a Rust project that provides a fast and memory-efficient way to read ABF (Axon Binary Format) files commonly used in electrophysiology.

Features

• Fast Reading: Utilizes optimized algorithms for quick ABF file parsing.
• Low Memory Footprint: Minimizes memory usage while processing large ABF files.
• Minimal Dependencies: Strives to keep dependencies lightweight.
• Easy to Use: Provides a simple API for reading ABF files.

Usage

1. Install Rust and Cargo if you haven't already.

2. Add this library to your Cargo.toml or using cargo add rust_abf

3. In your Rust code:

   use std::path::Path;
   use rust_abf::Abf;
   
   fn main() {
       let abf = Abf::from_file(Path::new("tests/test_abf/14o08011_ic_pair.abf")).unwrap();
       match abf {
           Ok(abf) => {
               let channels_count = abf.get_channels_count();
               let sweeps_count = abf.get_sweeps_count();
               println!("There are {:?} channels and {:?} sweeps", channels_count, sweeps_count);
               (0..channels_count).for_each(|ch| {
                   (0..sweeps_count).for_each(|s|{
                       let data = abf.get_sweep_in_channel( s, ch).unwrap();
                       println!("First 10 elements from ch {:?} and sweep {:?}: {:?}", ch, s, &data[0..10]);
                   });
               });
           },
           _ => println!("File not found"),
       }
   }
   

If you prefer to work on channels, you can have direct access to them by using the following code:

    ...
    let ch0 = abf.get_channel(0).unwrap();
    println!("Channel 0 has the following unit of measurement {:?} and the following label {:?}", ch0.get_uom(), ch0.get_label());
    for s in 0..abf.get_sweeps_count() {
        let data = ch0.get_sweep(s).unwrap();
        println!("Sweep {:?} has {:?} points", s, data.len());
    }
    ...

You might also prefer a more functional approach like the following:

    ...
    abf.get_channels()
        .for_each(|channel| {
            channel.get_sweeps()
            // take only the Some values
            .flatten()
            .for_each(|sweep| println!("First 10 elements {:?}, the unit of measurement is {:?}", &sweep[0..10], channel.get_uom()))
        });
    ...

Contributing

Contributions are welcome! If you encounter issues or have suggestions, please open an issue or submit a pull request.

License

This project is licensed under the MIT License. See the LICENSE file for details.