cuphaser

CuPy-based 3D phase retrieval for X-ray single particle imaging.

Installation

pip install cuphaser

GPU Support

CuPhaser runs on CPU by default (using NumPy). For GPU acceleration, install the appropriate CuPy package for your CUDA version:

# For CUDA 12.x
pip install "cuphaser[cuda12x]"

# For CUDA 13.x
pip install "cuphaser[cuda13x]"

Alternatively, install CuPy separately following the CuPy installation guide.

Optional Dependencies

# With FFTW support (faster CPU FFTs)
pip install "cuphaser[fftw]"

Development Installation

For development, clone the repository and install in editable mode:

git clone https://github.com/AyyerLab/CuPhaser.git
cd CuPhaser
pip install -e ".[dev]"

Requirements

• Python >= 3.8
• numpy, scipy, mrcfile, h5py
• PyQt5, matplotlib, pyqtgraph
• cupy (optional, for GPU acceleration)
• pyfftw (optional, for faster CPU FFTs)

Usage

Preprocessing (required for Dragonfly output)

If using output from Dragonfly, first preprocess it:

# Interactive GUI for preprocessing configuration
cuphaser.preprocess.gui config.ini

# Or run preprocessing from command line
cuphaser.preprocess config.ini

Phase Retrieval

cuphaser -c config.ini

Configuration

See sample.ini for a complete configuration example.

License

GPL-3.0