anwarnunez / pykilosort

[WIP] Python port of Kilosort 2

[WIP] Python port of KiloSort2

This is a work-in-progress litteral Python port of the original MATLAB version of Kilosort 2, written by Marius Pachitariu. The code is still being debugged and is not ready for use.

Hardware requirements

The code makes extensive use of the GPU via the CUDA framework. A high-end GPU with at least 8GB of memory is required. A good CPU and a large amount of RAM (minimum 32GB or 64GB) is also required.

Dependencies

• Python 3.7+
• NumPy
• SciPy
• CuPy
• matplotlib
• tqdm
• click
• pytest
• numba

Usage example

The programming interface is subject to change. The following code example should be saved in a directory, along with the following files:

• imec_385_100s.bin
• chanMap.npy (be careful with 0- and 1- indexing discrepancy between MATLAB and Python: don't forget to subtract 1 if this file was used in Kilosort)
• xc.npy
• yc.npy
• kcoords.npy

from pathlib import Path
import numpy as np

from pykilosort import add_default_handler, run, Bunch, read_data

add_default_handler(level='DEBUG')

dat_path = Path('imec_385_100s.bin')
dir_path = dat_path.parent

probe = Bunch()
probe.NchanTOT = 385

# WARNING: indexing mismatch with MATLAB hence the -1
probe.chanMap = np.load(dir_path / 'chanMap.npy').squeeze().astype(np.int64) - 1

probe.xc = np.load(dir_path / 'xc.npy').squeeze()
probe.yc = np.load(dir_path / 'yc.npy').squeeze()
probe.kcoords = np.load(dir_path / 'kcoords.npy').squeeze()

# The raw data file is loaded in Fortran order, its shape is therefore (n_channels, n_samples).
raw_data = read_data(dat_path, shape=(probe.NchanTOT, -1), dtype=np.int16)

run(dir_path, raw_data, probe, dat_path=dat_path)

Disk cache

The MATLAB version used a big rez structured object containing the input data, the parameters, intermediate and final results.

The Python version makes the distinction between:

• raw_data: a NumPy-like object of shape (n_channels_total, n_samples)
• probe: a Bunch instance (dictionary) with the channel coordinates, the indices of the "good channels"
• params: a Bunch instance (dictionary) with optional user-defined parameters. It can be empty. Any missing parameter is transparently replaced by the default as found in default_params.py file in the repository.
• intermediate: a Bunch instance (dictionary) with intermediate arrays.

These objects are accessible via the context (ctx) which replaces the MATLAB rez object: ctx.raw_data, etc.

This context also stores a special object called ctx.intermediate which stores intermediate arrays. This object derives from Bunch and implements special methods to save and load arrays in a temporary folder. By default, an intermediate result called ctx.intermediate.myarray is stored in ./.kilosort/context/myarray.npy.

The main run() function checks the existence of some of these intermediate arrays to skip some steps that might have run already, for a given dataset.

The suffixes _m (merge), _s (split), _c (cutoff) are used to disambiguate between multiple processing steps for the same arrays (they would be overwritten otherwise).

Technical notes about the port

The following differences between MATLAB and Python required special care during the port:

• Discrepancy between 0-based and 1-based indexing.
• MATLAB uses Fortran ordering for arrays, whereas NumPy uses C ordering by default. The Python code therefore uses Fortran ordering exclusively so that the custom CUDA kernels can be used with no modification.
• In MATLAB, arrays can be extended transparently with indexing, whereas NumPy/CuPy requires explicit concatenation.
• The MATLAB code used mex C files to launch CUDA kernels, whereas the Python code uses CuPy directly.
• A few workarounds around limitations of CuPy compared to MATLAB: no cp.median(), no GPU version of the lfilter() LTI filter in CuPy (a custom CUDA kernel had to be written), etc.