├── .github ├── pull_request_template.md └── workflows │ ├── pypi_publish.yml │ └── python-app.yml ├── .gitignore ├── .python-version ├── .readthedocs.yaml ├── LICENSE.txt ├── README.rst ├── docs ├── Makefile ├── requirements.txt └── source │ ├── api │ ├── enums.rst │ ├── index.rst │ ├── options.rst │ ├── task.rst │ └── utils.rst │ ├── conf.py │ ├── getting_started.rst │ ├── img │ ├── logo.png │ ├── pos_mapping_1.png │ ├── pos_mapping_2.png │ └── pos_mapping_3.png │ ├── index.rst │ └── using_pty_chi │ ├── data_structures.rst │ ├── devices.rst │ ├── engines.rst │ ├── index.rst │ ├── initialization_recommendations.rst │ ├── io.rst │ ├── position_mapping.rst │ └── reference.rst ├── examples └── save_movies.py ├── pyproject.toml ├── requirements.txt ├── src └── ptychi │ ├── __init__.py │ ├── api │ ├── __init__.py │ ├── enums.py │ ├── options │ │ ├── __init__.py │ │ ├── ad_general.py │ │ ├── ad_ptychography.py │ │ ├── base.py │ │ ├── bh.py │ │ ├── data.py │ │ ├── dm.py │ │ ├── lsqml.py │ │ ├── pie.py │ │ └── task.py │ ├── task.py │ └── types.py │ ├── data_structures │ ├── __init__.py │ ├── base.py │ ├── object.py │ ├── opr_mode_weights.py │ ├── parameter_group.py │ ├── probe.py │ └── probe_positions.py │ ├── device.py │ ├── forward_models.py │ ├── image_proc.py │ ├── io_handles.py │ ├── maps.py │ ├── maths.py │ ├── metrics.py │ ├── movies │ ├── __init__.py │ ├── api.py │ ├── io.py │ ├── mappings.py │ ├── movie_utils.py │ └── settings.py │ ├── parallel.py │ ├── position_correction.py │ ├── propagate.py │ ├── py.typed │ ├── reconstructors │ ├── __init__.py │ ├── ad_general.py │ ├── ad_ptychography.py │ ├── base.py │ ├── bh.py │ ├── dm.py │ ├── lsqml.py │ ├── nn │ │ ├── __init__.py │ │ ├── components.py │ │ └── models │ │ │ ├── autoencoder.py │ │ │ └── unet.py │ └── pie.py │ ├── timing │ ├── io.py │ └── timer_utils.py │ └── utils.py ├── tests ├── conftest.py ├── generate_gold_data_for_all.sh ├── test_2d_ptycho_affine_pos.py ├── test_2d_ptycho_autodiff.py ├── test_2d_ptycho_autodiff_multiprocess.py ├── test_2d_ptycho_bh.py ├── test_2d_ptycho_detector_size.py ├── test_2d_ptycho_dip.py ├── test_2d_ptycho_dm.py ├── test_2d_ptycho_epie.py ├── test_2d_ptycho_epie_mixed_states.py ├── test_2d_ptycho_epie_opr.py ├── test_2d_ptycho_epie_position_correction.py ├── test_2d_ptycho_lsqml.py ├── test_2d_ptycho_lsqml_compact.py ├── test_2d_ptycho_lsqml_momentum.py ├── test_2d_ptycho_lsqml_multiprocess.py ├── test_2d_ptycho_lsqml_multiscan.py ├── test_2d_ptycho_lsqml_uniform.py ├── test_2d_ptycho_mpie.py ├── test_2d_ptycho_near_field.py ├── test_2d_ptycho_opt_plan.py ├── test_2d_ptycho_probe_power_constraint.py ├── test_2d_ptycho_rpie_synthesisdictlearn.py ├── test_2d_ptycho_smoothness_constraint.py ├── test_data_on_gpu.py ├── test_maths.py ├── test_multislice_ptycho_autodiff.py ├── test_multislice_ptycho_autodiff_multigpu.py ├── test_multislice_ptycho_autodiff_regularized.py ├── test_multislice_ptycho_autodiff_slice_spacing_opt.py ├── test_multislice_ptycho_lsqml.py ├── test_multislice_ptycho_lsqml_joint_step_size.py ├── test_multislice_ptycho_lsqml_nonsq_psize.py ├── test_multislice_ptycho_lsqml_regularized.py ├── test_multislice_ptycho_rpie_synthesisdictlearn.py ├── test_patch_extraction_placement.py ├── test_ptycho_dp_blur.py ├── test_ptycho_low_mem_forward_model.py ├── test_remove_grid_artifacts.py └── test_utils.py └── uv.lock /.github/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/pty-chi/HEAD/.github/pull_request_template.md -------------------------------------------------------------------------------- /.github/workflows/pypi_publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/pty-chi/HEAD/.github/workflows/pypi_publish.yml 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