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:

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]]