etomofiles 0.1.1

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.

Installation

pip install etomofiles

Quick Start

import etomofiles

# 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

xf Utilities

Get xf as numpy array:

import etomofiles

# Read alignment data
df = etomofiles.read("TS_001/")

# Get xf as numpy array:
xf_matrices = etomofiles.df_to_xf(df)

# Each matrix represents an affine transformation:
# [[A11, A12, DX],
#  [A21, A22, DY]]
# where X' = A11*X + A12*Y + DX
#       Y' = A21*X + A22*Y + DY

# Also works directly with files
xf_matrices = etomofiles.df_to_xf("TS_001/TS_001.xf")

# Choose row ordering convention
xf_xy = etomofiles.df_to_xf(df)  # default xy
# Each matrix is [[A11, A12, DX], [A21, A22, DY]]

xf_yx = etomofiles.df_to_xf(df, yx=True)  # yx
# Each matrix is [[A22, A21, DY], [A12, A11, DX]]