etomofiles 0.1.0

A Python package for reading IMOD etomo alignment files into pandas DataFrames

etomofiles

A Python package for reading IMOD etomo alignment files into pandas DataFrames.

Overview

etomofiles provides a way to extract metadata from etomo alignment directories and convert them into structured pandas DataFrames.

Requirements

• Python ≥ 3.10
• numpy ≥ 1.19.0
• pandas ≥ 1.3.0
• mrcfile ≥ 1.3.0

Quick Start

import etomofiles
from pathlib import Path

# Read etomo alignment data
df = etomofiles.read("/path/to/etomo/directory")

print(df.head())

DataFrame Columns

The resulting DataFrame contains the following columns:

Column	Description
image_path	Path to specific image in tilt series (e.g., TS_001.st[0])
idx_tilt	Index of the tilt image (0-based)
tilt_axis_angle	Tilt axis rotation angle (degrees)
rawtlt	Raw tilt angle (degrees)
tlt	Corrected tilt angle (degrees)
xtilt	Tilt around x-axis
xf_a11, xf_a12, xf_a21, xf_a22, xf_dx, xf_dy	xf transformation matrix elements
excluded	Boolean indicating if view was excluded