(reference:workflow)=

# Workflow

This section contains example notebooks demonstrating common
PtyRAD workflow.

```{toctree}
:maxdepth: 1
:hidden:

run_ptyrad
read_ptyrad_output_hdf5
get_affine_from_image
get_error_distribution
get_local_obj_tilts
get_reconstruction_provenance
```

## Getting Started
{doc}`run_ptyrad` — Quickstart to run your first PtyRAD reconstruction.

{doc}`read_ptyrad_output_hdf5` — How to load, read, and parse PtyRAD HDF5 outputs.

## Analysis
{doc}`get_affine_from_image` — Calculate affine matrices to correct scan distortions.

{doc}`get_error_distribution` — Diagnostics for error distributions.

{doc}`get_local_obj_tilts` — Extract local object tilts.

## Reproducibility
{doc}`get_reconstruction_provenance` — Recover full reconstruction history from sequential runs.