alnfile 0.1.1

A Python package for reading AreTomo alignment files into pandas DataFrames.

alnfile

A Python package for reading AreTomo alignment files into pandas DataFrames, with utilities for converting to IMOD transformation matrices.

Installation

pip install alnfile

Quick start

Basic usage

The main function is alnfile.read() which accepts a file path and an optional alignment type:

import alnfile

# Read either global or local alignments (default global)
global_df = alnfile.read("path/to/your/file.aln")
print(global_df.head())
# Columns: sec, rot, gmag, tx, ty, smean, sfit, scale, base, tilt

# Local alignments   
local_df = alnfile.read("file.aln", alignment_type="local")
print(local_df.head())
# Columns: sec_idx, patch_idx, center_x, center_y, shift_x, shift_y, is_reliable

IMOD Transformation Matrices

Convert alignment data to IMOD-compatible transformation matrices:

import alnfile

# Read alignment data
df = alnfile.read("path/to/your/file.aln")

# Convert DataFrame to transformation matrices (IMOD .xf format)
xf_matrices = alnfile.df_to_xf(df)  # Returns (n_tilts, 2, 3) array
# Each matrix is [[A11, A12, DX], [A21, A22, DY]]

# Use yx convention (swap rows) if needed for specific applications
xf_matrices_yx = alnfile.df_to_xf(df, yx=True)  # Returns (n_tilts, 2, 3) array
# Each matrix is [[A22, A21, DY], [A12, A11, DX]]

Data Structure

Global Alignment DataFrame

Column	Type	Description
sec	int	Zero-indexed position in the final aligned stack (excludes dark frames)
rot	float	Rotation angle of the tilt axis relative to Y-axis (degrees)
gmag	float	Global magnification adjustment factor
tx	float	X shift (pixels)
ty	float	Y shift (pixels)
smean	float	Statistical metric (implementation-specific, see AreTomo docs)
sfit	float	Statistical metric (implementation-specific, see AreTomo docs)
scale	float	Scaling parameter for this tilt
base	float	Implementation-specific parameter (see AreTomo docs)
tilt	float	Nominal tilt angle (degrees)

Local Alignment DataFrame

Column	Type	Description
sec_idx	int	Tilt position in final tilt series stack, zero-indexed (post dark frame removal)
patch_idx	int	Sequential patch identifier within this tilt image (zero-indexed)
center_x	float	Expected x position of patch center relative to image center (pixels)
center_y	float	Expected y position of patch center relative to image center (pixels)
shift_x	float	Measured x deviation from expected patch position (pixels)
shift_y	float	Measured y deviation from expected patch position (pixels)
is_reliable	float	Confidence flag for patch alignment quality (1.0=reliable, 0.0=unreliable)

Rows will have None values for columns not applicable to their type.

Attribution

This implementation has been adapted from a similar reader in cryoet-alignment repository by Utz H. Ermel (@uermel).