├── .github └── workflows │ └── test.yml ├── CHANGELOG.md ├── LICENSE-APACHE ├── LICENSE-MIT ├── README.md ├── code_of_conduct.md ├── docs ├── .gitignore ├── build-docs.sh ├── flydra-sphinx-docs │ ├── .gitignore │ ├── FAQ.rst │ ├── Makefile │ ├── README │ ├── analysis_map.dot │ ├── analysis_map.png │ ├── analysis_map.sh │ ├── calibrating.md │ ├── calibration.rst │ ├── clean-build-and-upload.sh │ ├── conf.py │ ├── data_analysis.rst │ ├── dataflow.dot │ ├── download-numpy-doc-sphinxext.sh │ ├── ext │ │ ├── LICENSE.txt │ │ ├── MANIFEST.in │ │ ├── README.txt │ │ ├── __init__.py │ │ ├── autosummary.py │ │ ├── autosummary_generate.py │ │ ├── comment_eater.py │ │ ├── compiler_unparse.py │ │ ├── docscrape.py │ │ ├── docscrape_sphinx.py │ │ ├── numpydoc.py │ │ ├── only_directives.py │ │ ├── phantom_import.py │ │ ├── plot_directive.py │ │ ├── setup.py │ │ ├── tests │ │ │ └── test_docscrape.py │ │ └── traitsdoc.py │ ├── flydra_sphinx_ext │ │ └── sourcelink_directive.py │ ├── gallery.rst │ ├── getting_started.rst │ ├── images │ │ ├── chessboard_geometry.png │ │ ├── chessboard_grid_no_mistakes.jpg │ │ ├── chessboard_grid_with_mistakes.jpg │ │ ├── chessboard_raw_found_corners.jpg │ │ ├── chessboard_rawbinary_found_corners.jpg │ │ ├── chessboard_undistorted_image.jpg │ │ ├── image-based-orientation.png │ │ └── image-based-orientation.svg │ ├── index.rst │ ├── install_notes.rst │ ├── modules.rst │ ├── modules │ │ ├── flydra_analysis.a2.benu.rst │ │ ├── flydra_analysis.a2.core_analysis.rst │ │ ├── flydra_analysis.a2.plot_kalman_2d.rst │ │ ├── flydra_analysis.a2.utils.rst │ │ ├── flydra_analysis.a2.xml_stimulus.rst │ │ ├── flydra_analysis.analysis.PQmath.rst │ │ ├── flydra_core.MainBrain.rst │ │ ├── flydra_core.geom.rst │ │ ├── flydra_core.kalman.dynamic_models.rst │ │ ├── flydra_core.kalman.flydra_tracker.rst │ │ └── flydra_core.reconstruct.rst │ ├── old │ │ ├── data2d_small.png │ │ ├── eth0_props.png │ │ ├── flydra.rst │ │ ├── flydra_topology.jpg │ │ ├── gimp_mask_example.png │ │ ├── mama_small.png │ │ ├── network_settings.png │ │ ├── network_setup.rst │ │ ├── overall_latency_20071115_baslerA602f.png │ │ ├── plot_kalman_2d_small.2.png │ │ ├── plot_kalman_2d_small.png │ │ └── running_flydra.rst │ ├── orientation_data.rst │ ├── orientation_ekf_fitter.rst │ ├── orientation_smoothing.rst │ ├── realtime_data.rst │ ├── rsync-it.sh │ ├── screenshots │ │ ├── flydra_analysis_calibration_align_gui.png │ │ ├── image_based_angles.jpg │ │ └── original │ │ │ └── flydra_analysis_calibration_align_gui.png │ └── trigger_device.rst ├── nose-0.11.1.tar.gz └── requirements.txt ├── flydra_analysis ├── .gitignore ├── MANIFEST.in ├── README.md ├── application-flydra-h5.sharedmimeinfo ├── conftest.py ├── flydra-plot-timeseries-2d-3d.mime ├── flydra_analysis │ ├── __init__.py │ ├── a2 │ │ ├── Makefile.kalmanize │ │ ├── __init__.py │ │ ├── aggdraw_coord_shifter.py │ │ ├── analysis_options.py │ │ ├── auto_discover_movies.py │ │ ├── auto_discover_ufmfs.py │ │ ├── benu.py │ │ ├── benu_colormaps.py │ │ ├── calculate_reprojection_errors.py │ │ ├── calculate_skipped_frames.py │ │ ├── calibration_align_gui.py │ │ ├── calibration_to_xml.py │ │ ├── check_clock_sync.py │ │ ├── check_frame_skip.py │ │ ├── check_mainbrain_h5_contiguity.py │ │ ├── conditions.py │ │ ├── conditions2.py │ │ ├── conditions_draw.py │ │ ├── core_analysis.py │ │ ├── data2smoothed.py │ │ ├── densities.py │ │ ├── experiment_layout.py │ │ ├── find_equiv_obj_id.py │ │ ├── find_long_trajectories.py │ │ ├── flydra_images_export.py │ │ ├── flydra_scons.py │ │ ├── flydra_textlog2csv.py │ │ ├── flypos.py │ │ ├── get_2D_image_latency.py │ │ ├── get_2D_image_latency_plot.py │ │ ├── get_clock_sync.py │ │ ├── h5_info.py │ │ ├── h5_shorten.py │ │ ├── image_based_orientation.py │ │ ├── kdmovie_saver.py │ │ ├── kdmovie_saver_default_path.kmp │ │ ├── kdviewer.py │ │ ├── lsprofcalltree.py │ │ ├── misc.py │ │ ├── missing_value_error.py │ │ ├── montage_ufmfs.py │ │ ├── orientation_ekf_fitter.py │ │ ├── orientation_ekf_plot.py │ │ ├── overlay_kalman_movie.py │ │ ├── plot_calibration_input.py │ │ ├── plot_camera_positions.py │ │ ├── plot_kalman_2d.py │ │ ├── plot_skipped_frames.py │ │ ├── plot_summary.py │ │ ├── plot_timeseries.py │ │ ├── plot_timeseries_2d_3d.py │ │ ├── plot_top_view.py │ │ ├── pos_ori2fu.py │ │ ├── print_kalmanize_makefile_location.py │ │ ├── print_reprojection_error.py │ │ ├── ransac.py │ │ ├── retrack_movies.py │ │ ├── retrack_reuse_data_association.py │ │ ├── revert_schema12_to_schema11.py │ │ ├── rosbag2flydrah5.py │ │ ├── sample_bowl.xml │ │ ├── sample_calibration.xml │ │ ├── sample_calibration_water.xml │ │ ├── sample_datafile-v0.4.28.h5 │ │ ├── sample_datafile-v0.4.28.h5.retracked.h5 │ │ ├── sample_datafile.h5.spreadh5 │ │ ├── sample_kalman_trajectories.h5 │ │ ├── sample_one_meter_cylinder_arena.xml │ │ ├── sample_stim_cubic_arena.xml │ │ ├── save_movies_overlay.py │ │ ├── stim_plugins.py │ │ ├── stimulus_positions.py │ │ ├── tables_tools.py │ │ ├── trajectory_filtering.py │ │ ├── ufmf_tools.py │ │ ├── utils.py │ │ ├── water_surface_align.py │ │ └── xml_stimulus.py │ ├── analysis │ │ ├── PQmath.py │ │ ├── __init__.py │ │ ├── caching_movie_opener.py │ │ ├── calc_forces.py │ │ ├── cam_params_play.py │ │ ├── circstats.py │ │ ├── copy_data_files.sh │ │ ├── copy_data_files_local.sh │ │ ├── create_movie.sh │ │ ├── flydra_analysis_convert_to_mat.py │ │ ├── flydra_analysis_filter_kalman_data.py │ │ ├── flydra_analysis_generate_recalibration.py │ │ ├── flydra_analysis_plot_clock_drift.py │ │ ├── flydra_analysis_plot_kalman_2d_histogram.py │ │ ├── flydra_analysis_print_camera_summary.py │ │ ├── flydra_convert_table_add_point_id.py │ │ ├── hzgeom.py │ │ ├── move_data_files_local.sh │ │ ├── pqmath_angular_velocity_quaternion_play.py │ │ ├── reconstruct_orientation.py │ │ ├── result_utils.py │ │ ├── save_as_flydra_hdf5.py │ │ ├── setup_analysis_dir.sh │ │ ├── smdfile.py │ │ ├── smooth_position.m │ │ ├── smooth_position_micro_demo.py │ │ ├── test_smooth.m │ │ └── test_smooth_orientation.py │ ├── autogenerated │ │ ├── data2smoothed.mat │ │ ├── datafile2d.spreadh5 │ │ ├── kalmanized.h5 │ │ ├── mpl_markersize.png │ │ ├── plot_kalman_2d.png │ │ ├── plot_timeseries_2d.png │ │ ├── plot_timeseries_2d_3d.png │ │ └── plot_timeseries_2d_with_spread.png │ ├── image_compare.py │ ├── kalmanize.py │ ├── mpl_markersize.py │ ├── offline_data_save.py │ ├── talign.py │ ├── test_commands.py │ ├── test_geom.py │ ├── test_reconstruction.py │ └── version.py ├── flydra_fastfinder_help.pyx ├── pyproject.toml ├── setup.py ├── stdeb.cfg └── tests │ ├── sample_calibration │ ├── Cst.dat │ ├── Pmatrices.dat │ ├── Pst.dat │ ├── Res.dat │ ├── basename1.cal │ ├── basename1.rad │ ├── basename2.cal │ ├── basename2.rad │ ├── basename3.cal │ ├── basename3.rad │ ├── basename4.cal │ ├── basename4.rad │ ├── basename5.cal │ ├── basename5.rad │ ├── calibration_units.txt │ ├── cam1.points4cal.dat │ ├── cam2.points4cal.dat │ ├── cam3.points4cal.dat │ ├── cam4.points4cal.dat │ ├── cam5.points4cal.dat │ ├── camera1.Pmat.cal │ ├── camera2.Pmat.cal │ ├── camera3.Pmat.cal │ ├── camera4.Pmat.cal │ ├── camera5.Pmat.cal │ └── camera_order.txt │ ├── test_calculate_reprojection_errors.py │ ├── test_calibration_realignment.py │ ├── test_export_flydra_hdf5.py │ ├── test_previously_failing.py │ ├── test_pymvg.py │ ├── test_reconstruct.py │ └── test_result_utils.py ├── flydra_core ├── .gitignore ├── MANIFEST.in ├── README.md ├── attic │ ├── MainBrain.py │ ├── coordinate_receiver.py │ └── rosutils.py ├── conftest.py ├── flydra_core │ ├── .gitignore │ ├── Roots3And4.c │ ├── Roots3And4.h │ ├── _Roots3And4.pxd │ ├── _Roots3And4.pyx │ ├── __init__.py │ ├── _fastgeom.pxd │ ├── _fastgeom.pyx │ ├── _flydra_tracked_object.pyx │ ├── _mahalanobis.pxd │ ├── _mahalanobis.pyx │ ├── _pmat_jacobian.pxd │ ├── _pmat_jacobian.pyx │ ├── _pmat_jacobian_water.pxd │ ├── _pmat_jacobian_water.pyx │ ├── _reconstruct_utils.pyx │ ├── _refraction.pxd │ ├── _refraction.pyx │ ├── align.py │ ├── common_variables.py │ ├── data_descriptions.py │ ├── debuglock.py │ ├── flydra_server_art.ai │ ├── flydra_server_art.png │ ├── flydra_socket.py │ ├── geom.py │ ├── kalman │ │ ├── __init__.py │ │ ├── dynamic_models.py │ │ ├── ekf.py │ │ ├── flydra_kalman_utils.py │ │ ├── flydra_tracker.py │ │ ├── lsprofcalltree.py │ │ ├── ori_smooth.py │ │ └── point_prob.py │ ├── reconstruct.py │ ├── test_refraction.py │ ├── undistort.py │ ├── version.py │ └── water.py ├── pyproject.toml ├── setup.py ├── stdeb.cfg └── sympy_demo │ ├── mahal.history │ ├── mahalanobis_sympy_test.py │ ├── pinhole_jacobian_demo.py │ └── refraction_demo.py └── packaging ├── flydra_compat ├── .gitignore ├── flydra │ ├── MainBrain.py │ ├── __init__.py │ ├── analysis.py │ └── reconstruct.py ├── setup.py └── stdeb.cfg └── python-flydra └── debian ├── changelog ├── compat ├── control ├── rules └── source └── format /.github/workflows/test.yml: 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