eerfile 0.0.4

Read electron event representation (EER) files in Python

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.