Quick Start

Basic Reconstruction

The simplest reconstruction runs the command-line tool with a TOML configuration file:

./release/recon config.toml

If you call the binary with no arguments, it prints usage and generates a template config file:

./release/recon
# Generates: config_template.toml

Minimal Configuration

Here is a minimal TOML configuration for an unconstrained conjugate gradient reconstruction:

[[input]]
filename = "data/projections.tiff"
angles   = "data/angles.txt"
gamma    = 0

[output]
filename = "recon.tiff"

[recon_params]
max_iters  = 50
tol        = 1e-5
xtol       = 1e-5
recon_dims = [51, 511, 511]

Configuration Explanation

  • [[input]] — Array-of-tables block containing one dataset. The double brackets mean you can have multiple inputs (for multi-tilt XMCD).

    • filename: Path to a TIFF file with projection data

    • angles: Path to a text file with one projection angle per line (degrees or radians, auto-detected)

    • gamma: Tilt angle in degrees (required, e.g., 0, ±45 for multi-tilt)

  • [output] — Output settings

    • filename: Where to save the reconstructed volume

  • [recon_params] — Reconstruction parameters

    • max_iters: Maximum iterations (default: 100)

    • tol: Loss convergence tolerance

    • xtol: Solution-change convergence tolerance

    • recon_dims: [thickness, height, width] in voxels

      • All dimensions must be odd

      • thickness is laminography depth (expected << width)

Input Data

Projection Data (TIFF)

The projection file should be a TIFF containing 2D projections, either as a single multi-frame image or as individual frames.

Angles File

Create a text file with one angle per line:

0.0
1.5
3.0
4.5
...

Angles can be in degrees or radians; the library auto-detects based on magnitude (max(|angle|) > 2π → degrees).

Alternatively, generate angles with the helper script:

scripts/angles.sh 0 90 > angles.txt

This creates angles from 0° to 90°.

Example: Multi-tilt XMCD

For multi-tilt magnetic circular dichroism, provide multiple inputs with different gamma angles:

[[input]]
filename = "data/projections_0.tiff"
angles   = "data/angles.txt"
gamma    = 0

[[input]]
filename = "data/projections_45.tiff"
angles   = "data/angles.txt"
gamma    = 45

[[input]]
filename = "data/projections_-45.tiff"
angles   = "data/angles.txt"
gamma    = -45

[output]
filename = "recon.tiff"

[recon_params]
max_iters  = 100
tol        = 1e-5
xtol       = 1e-5
recon_dims = [51, 511, 511]

Next Steps