Crate fpm_rs 

Image-plane Fourier ptychographic microscopy (FPM) reconstruction and simulation.

The crate separates experimental geometry from numerical reconstruction. A typical workflow is:

1. describe the microscope with experiment::Optics and an illumination source such as experiment::PlanarLedArray, plus calibration and acquisition;
2. compile that description into an algorithm-facing model::ImagePlaneModel;
3. pair the model with resident or lazy measurements in a reconstruction::ReconstructionProblem;
4. select an algorithms implementation and run it directly or through a reconstruction::Runner;
5. inspect the complex object, amplitude, phase, pupil, trace, and diagnostics in the resulting reconstruction::ReconstructionResult; and
6. optionally create controlled data with simulation, calculate metrics, or persist result and benchmark bundles through reconstruction::ResultBundle and benchmark.

Experimental coordinates and detector arrays use explicit conventions documented on their types. Two-dimensional arrays are generally indexed (row, column) and shaped (height, width); transverse wave vectors are (kx, ky) in radians per metre.

Example

use fpm_rs::{
    algorithms::{AlternatingProjection, ReconstructionAlgorithm},
    experiment::{ArrayPose, Illumination, Optics, PlanarLedArray},
    measurements::{FrameMetadata, MeasurementStack},
    model::{ImagePlaneModel, ReconstructionShape},
    reconstruction::ReconstructionProblem,
};
use ndarray::Array3;

let optics = Optics {
    wavelength_vacuum_m: 532e-9,
    objective_na: 0.1,
    magnification: 4.0,
    camera_pixel_size: 6.5e-6,
    illumination_refractive_index: 1.0,
    objective_medium_refractive_index: 1.0,
    defocus_distance: None,
    pupil_aberration: None,
};
let illumination = Illumination::from_geometry(PlanarLedArray::new(
    (1, 1),
    (4e-3, 4e-3),
    (0.0, 0.0),
    ArrayPose::from_translation([0.0, 0.0, -90e-3]),
))?;
let model = ImagePlaneModel::from_experiment(
    &optics,
    &illumination,
    (4, 4),
    ReconstructionShape::Exact((4, 4)),
)?;
let measurements = MeasurementStack::new(
    Array3::from_elem((1, 4, 4), 1.0),
    vec![FrameMetadata::new(0)],
)?;
let problem = ReconstructionProblem::new(measurements, model)?;
let result = AlternatingProjection::default().iterations(1).run(&problem)?;
assert_eq!(result.object.dim(), (4, 4));

Re-exports

pub use benchmark_bundle::BenchmarkBundle;

pub use benchmark_bundle::read_benchmark_bundle;

pub use error::Error;

pub use error::Result;

pub use reconstruction::ResultBundle;

pub use reconstruction::read_bundle;

Modules

algorithms

Reconstruction algorithms and their shared execution contract. Iterative reconstruction algorithms for compiled image-plane models.

backend

CPU execution and the interfaces used by future resident-buffer backends. Execution backends and resident-buffer abstractions.

benchmark

Reproducible single-case reconstruction benchmarks.

benchmark_bundle

Normalized benchmark comparison bundles.

callbacks

Iteration callbacks for progress, checkpoints, diagnostics, and image output. Hooks that observe or control iterative reconstruction.

complex

Utilities for complex fields, amplitude, and wrapped phase. Allocation-aware helpers for two-dimensional complex sample fields.

configuration

Versioned experiment and simulation configuration.

datasets

Loading, discovery, caching, and subsetting for converted dataset bundles.

diagnostics

Structured iteration and per-frame reconstruction diagnostics. Structured convergence, coverage, and per-frame reconstruction diagnostics.

error

Error categories and the crate-wide error::Result alias. Error categories returned by validation, numerical, I/O, and bundle operations.

evaluation

Composed evaluation of a reconstruction against reference data.

experiment

Physical optics and illumination geometry compiled into numerical models. Physical optics and illumination descriptions for an image-plane experiment.

illumination_calibration

Bounded physical planar-array calibration configuration, state, and diagnostics. Bounded physical calibration of planar LED-array illumination.

illumination_initialization

Bright-field circle initialization for bounded physical planar arrays. Bright-field circle initialization for physical planar LED arrays.

measurements

Resident and lazy low-resolution intensity measurement stacks. Low-resolution measured-intensity stacks and acquisition metadata.

metrics

Reusable numerical metrics, organized by the meaning of their inputs.

model

Compiled image-plane models, Fourier crops, pupils, and forward propagation. Compiled image-plane forward model used by simulation and reconstruction.

reconstruction

Reconstruction problems, state, schedules, runners, results, and checkpoints. Reconstruction inputs, execution state, schedules, checkpoints, and results.

simulation

Synthetic objects, camera response, acquisition effects, and simulation. Controlled synthetic acquisition for image-plane Fourier ptychography.

tabular

On-demand Polars conversions for reconstruction and benchmark records.

Type Aliases

Complex64

Alias for a Complex<f64>