├── .gitattributes ├── .github └── workflows │ ├── test-conda.yml │ └── test-pip.yml ├── .gitignore ├── .travis.yml ├── .zenodo.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmarks ├── benchmarks.db ├── benchmarks.py ├── maxima_benchmarks.ipynb ├── numba_benchmarks.ipy ├── simple_benchmarks.ipy ├── source │ └── vbench │ │ ├── figures │ │ └── locate_artificial_sparse.png │ │ └── locate_artificial_sparse.txt ├── suite.py └── test_perf.py ├── doc ├── Makefile ├── _static │ └── .gitignore ├── _templates │ └── autosummary │ │ └── class.rst ├── api.rst ├── conf.py ├── featured-thumbnails │ ├── fluorescent-particles-in-cfs.png │ ├── foam.png │ ├── interfacial-particles.png │ ├── large-particle-in-liquid-crystal.png │ ├── rearrangements-and-strain.png │ ├── tracking-sphere.png │ └── trajectories-in-water.png ├── index.rst ├── installation.rst ├── introduction.rst ├── releases │ ├── v0.3.0.txt │ ├── v0.3.1.txt │ ├── v0.4.txt │ ├── v0.5.txt │ ├── v0.6.txt │ └── v0.7.txt ├── tutorial.rst ├── tutorial │ ├── Makefile │ └── tools │ │ ├── nb_to_doc.py │ │ └── nbstripout └── whatsnew.rst ├── doi.png ├── examples └── README.md ├── reproducibility_data.py ├── setup.cfg ├── setup.py ├── soft-matter-docs-deploy.enc ├── test_perf.sh ├── trackpy ├── __init__.py ├── _version.py ├── api.py ├── artificial.py ├── diag.py ├── feature.py ├── filtering.py ├── find.py ├── framewise_data.py ├── linking │ ├── __init__.py │ ├── find_link.py │ ├── legacy.py │ ├── linking.py │ ├── partial.py │ ├── subnet.py │ ├── subnetlinker.py │ └── utils.py ├── locate_functions │ ├── __init__.py │ └── brightfield_ring.py ├── masks.py ├── motion.py ├── plots.py ├── predict.py ├── preprocessing.py ├── refine │ ├── __init__.py │ ├── brightfield_ring.py │ ├── center_of_mass.py │ └── least_squares.py ├── static.py ├── tests │ ├── README.rst │ ├── __init__.py │ ├── common.py │ ├── data │ │ ├── reproduce_duplicate_track_assignment.npy │ │ ├── reproducibility_v0.4.npz │ │ └── sparse_trajectories.npy │ ├── locate │ │ └── test_brightfield_ring.py │ ├── test_correlations.py │ ├── test_feature.py │ ├── test_feature_saving.py │ ├── test_find.py │ ├── test_find_link.py │ ├── test_leastsq.py │ ├── test_legacy_linking.py │ ├── test_linking.py │ ├── test_mask.py │ ├── test_misc.py │ ├── test_motion.py │ ├── test_plot_traj_labeling.py │ ├── test_plots.py │ ├── test_predict.py │ ├── test_preprocessing.py │ ├── test_reproducibility.py │ ├── test_static.py │ ├── video │ │ ├── bulk-water_frame0.npy │ │ ├── bulk-water_frame1.npy │ │ ├── image_sequence │ │ │ ├── T76S3F00001.png │ │ │ ├── T76S3F00002.png │ │ │ ├── T76S3F00003.png │ │ │ ├── T76S3F00004.png │ │ │ └── T76S3F00005.png │ │ ├── seq_frame0.npy │ │ ├── seq_frame1.npy │ │ ├── stuck.tif │ │ ├── stuck_frame0.npy │ │ └── stuck_frame1.npy │ ├── water │ │ └── bulk-water.mov │ └── wire │ │ ├── horizontal expected result.png │ │ ├── horizontal_frame.npy │ │ ├── oblique expected result.png │ │ ├── oblique_frame.npy │ │ ├── vertical expected result.png │ │ └── vertical_frame.npy ├── tracking.py ├── try_numba.py ├── uncertainty.py └── utils.py └── versioneer.py /.gitattributes: -------------------------------------------------------------------------------- 1 | trackpy/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/workflows/test-conda.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/soft-matter/trackpy/HEAD/.github/workflows/test-conda.yml -------------------------------------------------------------------------------- /.github/workflows/test-pip.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/soft-matter/trackpy/HEAD/.github/workflows/test-pip.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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