eerfile

Read electron event representation (EER) files as NumPy arrays in Python.

Installation

eerfile is available on PyPI and can be installed with pip

pip install eerfile

Usage

import eerfile

# render multi-frame micrograph from file and target dose per frame
# dose per frame is in electrons per square angstrom
image = eerfile.render("FoilHole_19622436.eer", dose_per_output_frame=1.0, total_fluence=50.0)

# or you can read the entire stack of EER frames
eer_frames = eerfile.read("FoilHole_19622436.eer")

Memory-Efficient Rendering

For large movies that may cause memory issues, you can specify a chunk size of the output frames to process frames in smaller batches:

import eerfile

# Memory-efficient rendering with chunking
# Processes frames in chunks to avoid memory overflow
image = eerfile.render(
    "large_movie.eer", 
    dose_per_output_frame=1.0,
    total_fluence=50.0,
    chunk_size=10      # Process 10 output frames at a time
)

Acknowledgements

This package is a very thin convenience layer on top of tifffile which provides the EER frame decoding logic.