├── .devcontainer └── devcontainer.json ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── dependabot.yml ├── linters │ └── .flake8 ├── scripts │ └── update_version.py └── workflows │ ├── black.yml │ ├── build-flake.yml │ ├── check_install_dev.yml │ ├── check_install_main.yml │ ├── check_install_quick.yml │ └── linter.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTORS.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ ├── Advanced_plots.png │ ├── DOE_logo.png │ ├── DOI-BADGE-978-3-319-76207-4_15.svg │ ├── demo.gif │ ├── dp.png │ ├── py4DSTEM_logo.png │ ├── py4DSTEM_logo_small.ico │ ├── py4DSTEM_logo_vsmall.ico │ └── toyota_research_institute.png ├── make.bat ├── papers.md ├── requirements.txt └── source │ ├── 4dstem.rst │ ├── acknowledgements.rst │ ├── api.rst │ ├── api │ ├── classes.rst │ ├── emd.rst │ ├── io.rst │ ├── io.rst.bk │ ├── preprocess.rst │ ├── process.rst │ ├── py4DSTEM.rst │ └── visualize.rst │ ├── apiindex.rst │ ├── conf.py │ ├── examples.rst │ ├── gplv3.txt │ ├── gui.rst │ ├── index.rst │ ├── installation.rst │ ├── license.rst │ ├── references.rst │ └── supportAndContributions.rst ├── images ├── DOE_logo.png ├── py4DSTEM_logo.png ├── py4DSTEM_logo_54_export.png └── toyota_research_institute.png ├── py4DSTEM ├── __init__.py ├── braggvectors │ ├── __init__.py │ ├── braggvector_methods.py │ ├── braggvectors.py │ ├── diskdetection.py │ ├── diskdetection_aiml.py │ ├── diskdetection_aiml_cuda.py │ ├── diskdetection_cuda.py │ ├── diskdetection_parallel.py │ ├── diskdetection_parallel_new.py │ ├── kernels.py │ ├── multicorr_col_kernel.cu │ ├── multicorr_row_kernel.cu │ ├── probe.py │ └── threshold.py ├── data │ ├── __init__.py │ ├── calibration.py │ ├── data.py │ ├── diffractionslice.py │ ├── propagating_calibration.py │ ├── qpoints.py │ └── realslice.py ├── datacube │ ├── __init__.py │ ├── datacube.py │ ├── virtualdiffraction.py │ └── virtualimage.py ├── io │ ├── __init__.py │ ├── filereaders │ │ ├── README.md │ │ ├── __init__.py │ │ ├── empad.py │ │ ├── read_K2.py │ │ ├── read_abTEM.py │ │ ├── read_arina.py │ │ ├── read_dm.py │ │ └── read_mib.py │ ├── google_drive_downloader.py │ ├── importfile.py │ ├── legacy │ │ ├── __init__.py │ │ ├── legacy12 │ │ │ ├── __init__.py │ │ │ ├── read_utils_v0_12.py │ │ │ ├── read_utils_v0_5.py │ │ │ ├── read_utils_v0_6.py │ │ │ ├── read_utils_v0_7.py │ │ │ ├── read_utils_v0_9.py │ │ │ ├── read_v0_12.py │ │ │ ├── read_v0_5.py │ │ │ ├── read_v0_6.py │ │ │ ├── read_v0_7.py │ │ │ └── read_v0_9.py │ │ ├── legacy13 │ │ │ ├── __init__.py │ │ │ ├── v13_emd_classes │ │ │ │ ├── __init__.py │ │ │ │ ├── array.py │ │ │ │ ├── io.py │ │ │ │ ├── metadata.py │ │ │ │ ├── pointlist.py │ │ │ │ ├── pointlistarray.py │ │ │ │ ├── root.py │ │ │ │ └── tree.py │ │ │ ├── v13_py4dstem_classes │ │ │ │ ├── __init__.py │ │ │ │ ├── braggvectors.py │ │ │ │ ├── calibration.py │ │ │ │ ├── datacube.py │ │ │ │ ├── diffractionslice.py │ │ │ │ ├── io.py │ │ │ │ ├── parenttree.py │ │ │ │ ├── probe.py │ │ │ │ ├── qpoints.py │ │ │ │ ├── realslice.py │ │ │ │ ├── virtualdiffraction.py │ │ │ │ └── virtualimage.py │ │ │ └── v13_to_14.py │ │ ├── read_legacy_12.py │ │ ├── read_legacy_13.py │ │ └── read_utils.py │ ├── parsefiletype.py │ ├── read.py │ └── save.py ├── preprocess │ ├── __init__.py │ ├── darkreference.py │ ├── electroncount.py │ ├── preprocess.py │ ├── radialbkgrd.py │ └── utils.py ├── process │ ├── __init__.py │ ├── calibration │ │ ├── __init__.py │ │ ├── ellipse.py │ │ ├── origin.py │ │ ├── probe.py │ │ ├── qpixelsize.py │ │ └── rotation.py │ ├── classification │ │ ├── __init__.py │ │ ├── braggvectorclassification.py │ │ ├── classutils.py │ │ └── featurization.py │ ├── diffraction │ │ ├── WK_scattering_factors.py │ │ ├── __init__.py │ │ ├── crystal.py │ │ ├── crystal_ACOM.py │ │ ├── crystal_bloch.py │ │ ├── crystal_calibrate.py │ │ ├── crystal_phase.py │ │ ├── crystal_viz.py │ │ ├── digital_dark_field.py │ │ ├── flowlines.py │ │ ├── tdesign.py │ │ └── utils.py │ ├── fit │ │ ├── __init__.py │ │ └── fit.py │ ├── phase │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── direct_ptychography.py │ │ ├── dpc.py │ │ ├── magnetic_ptychographic_tomography.py │ │ ├── magnetic_ptychography.py │ │ ├── mixedstate_multislice_ptychography.py │ │ ├── mixedstate_ptychography.py │ │ ├── multislice_ptychography.py │ │ ├── parallax.py │ │ ├── parameter_optimize.py │ │ ├── phase_base_class.py │ │ ├── ptychographic_constraints.py │ │ ├── ptychographic_methods.py │ │ ├── ptychographic_tomography.py │ │ ├── ptychographic_visualizations.py │ │ ├── singleslice_ptychography.py │ │ ├── utils.py │ │ └── xray_magnetic_ptychography.py │ ├── polar │ │ ├── __init__.py │ │ ├── polar_analysis.py │ │ ├── polar_datacube.py │ │ ├── polar_fits.py │ │ └── polar_peaks.py │ ├── rdf │ │ ├── __init__.py │ │ ├── amorph.py │ │ └── rdf.py │ ├── strain │ │ ├── __init__.py │ │ ├── latticevectors.py │ │ └── strain.py │ ├── utils │ │ ├── __init__.py │ │ ├── cluster.py │ │ ├── cross_correlate.py │ │ ├── elliptical_coords.py │ │ ├── masks.py │ │ ├── multicorr.py │ │ ├── scattering_factors.txt │ │ ├── single_atom_scatter.py │ │ └── utils.py │ └── wholepatternfit │ │ ├── __init__.py │ │ ├── wp_models.py │ │ ├── wpf.py │ │ └── wpf_viz.py ├── utils │ ├── __init__.py │ └── configuration_checker.py ├── version.py └── visualize │ ├── README.md │ ├── __init__.py │ ├── overlay.py │ ├── show.py │ ├── show_extention.py │ ├── vis_RQ.py │ ├── vis_grid.py │ └── vis_special.py ├── setup.cfg ├── setup.py └── test ├── README.md ├── download_test_data.py ├── gettestdata.py ├── test_braggvectors.py ├── test_calibration.py ├── test_crystal.py ├── test_datacube.py ├── test_import.py ├── test_misc.py ├── test_native_io ├── test_calibration_io.py ├── test_listwrite.py ├── test_realslice_read.py ├── test_single_object_io.py ├── test_v0_13.py ├── test_v0_14.py └── test_v0_9.py ├── 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