├── .gitignore ├── .openworm.yml ├── .travis.yml ├── LICENSE.md ├── README.md ├── THANKS.md ├── documentation ├── INSTALL-OSX.md ├── INSTALL.md ├── Movement Validation White Paper.md ├── OpenWorm Analysis Toolbox logo.png ├── Project History.md ├── Schafer_validation │ ├── Issues with WT2 Analysis Toolbox 1.3.4.md │ ├── N2_A_24C_L_5_2015_06_16__19_54_27___feat_comparison.pdf │ ├── N2_A_24C_R_4_2015_06_16__19_22_48___feat_comparison.pdf │ ├── Notes on original WT2 Schafer code.md │ └── frame_codes.csv ├── Worm Tracking Sources and Tools.md ├── data_examples.md ├── database schema │ ├── CSV │ │ ├── DataTypes.csv │ │ ├── FeatureSpecifications.csv │ │ └── FieldDescriptions.csv │ ├── Features Specifications.xlsx │ ├── Schema - MRC DB.mwb │ ├── Schema - MRC DB.png │ ├── Schema - Multi-Worm.erwin │ ├── Schema - Multi-Worm.pdf │ └── Schema - Multi-Worm.sql ├── dependency_notes.md ├── feature_descriptions │ ├── Absolute Coordinates.md │ ├── Feature File Overview.md │ ├── Feature Overview.md │ ├── Locomotion - basic tree.gif │ ├── Locomotion - bends.gif │ ├── Locomotion - motion.gif │ ├── Locomotion - turns.gif │ ├── Locomotion - velocity.gif │ ├── Locomotion.md │ ├── Morphology.md │ ├── Path Figure.gif │ ├── Path.md │ ├── Phenotypic Ontology.md │ ├── Posture.md │ ├── ReadMe.md │ ├── Supplementary Figure 1.gif │ ├── Supplementary Figure 2.gif │ ├── Supplementary Figure 3.gif │ ├── Supplementary Figure 4.gif │ ├── Supplementary Figure 5.gif │ ├── Supplementary Figure 6.gif │ ├── Ventral Side Annotation and Head Detection.md │ ├── Worm Segmentation.md │ ├── body part locations.gif │ ├── eigenworms.png │ ├── fig 4 b - bend angle.gif │ ├── fig 4 c and d - velocity.gif │ ├── fig 4 e - crawling.gif │ ├── fig 4 f - motion states.gif │ ├── fig 4 g - foraging.gif │ ├── fig 4 h - range.gif │ ├── fig 4 i - dwelling.gif │ ├── s1.md │ ├── s2.md │ ├── s3.md │ ├── s4.md │ ├── s5.md │ ├── s6.md │ └── skeleton_lengths_interpolated.gif └── pypi_notes.md ├── examples ├── WCON demo.py ├── __init__.py ├── feature_subset_example.py ├── generate_stats.py ├── generate_stats_plots.py ├── plot_eigenworms.py ├── plot_example.py └── video_to_features.py ├── open_worm_analysis_toolbox ├── __init__.py ├── config.py ├── features │ ├── __init__.py │ ├── events.py │ ├── feature_manipulations.py │ ├── feature_metadata │ │ ├── __init__.py │ │ ├── features_list.csv │ │ ├── features_list_definitions.txt │ │ └── old_features_comparison_notes.csv │ ├── feature_processing_options.py │ ├── generic_features.py │ ├── locomotion_bends.py │ ├── locomotion_features.py │ ├── locomotion_turns.py │ ├── master_eigen_worms_N2.mat │ ├── morphology_features.py │ ├── path_features.py │ ├── posture_features.py │ ├── velocity.py │ └── worm_features.py ├── prefeatures │ ├── __init__.py │ ├── basic_worm.py │ ├── normalized_worm.py │ ├── pre_features.py │ ├── pre_features_helpers.py │ ├── skeleton_calculator1.py │ ├── video_info.py │ └── worm_plotter.py ├── statistics │ ├── __init__.py │ ├── feature_metadata │ │ ├── __init__.py │ │ ├── event_features.csv │ │ ├── event_features_2.csv │ │ ├── movement_features.csv │ │ ├── simple_features.csv │ │ └── simple_features_2.csv │ ├── histogram.py │ ├── histogram_manager.py │ ├── pathplot.py │ ├── pathplot_manager.py │ ├── specifications.py │ └── statistics_manager.py ├── travis_config.txt ├── user_config_example.txt ├── utils.py └── version.py ├── setup.py ├── tests ├── ReadMe.md ├── test_areas.py ├── test_features.py ├── test_pre_features.py ├── test_spec_filtering.py ├── unit_test1.py └── validate_features.py └── tools ├── install-ubuntu-cleanvm.sh └── test_setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/.gitignore -------------------------------------------------------------------------------- /.openworm.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/.openworm.yml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/README.md -------------------------------------------------------------------------------- /THANKS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/THANKS.md -------------------------------------------------------------------------------- /documentation/INSTALL-OSX.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/INSTALL-OSX.md -------------------------------------------------------------------------------- /documentation/INSTALL.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/INSTALL.md -------------------------------------------------------------------------------- /documentation/Movement Validation White Paper.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Movement Validation White Paper.md -------------------------------------------------------------------------------- /documentation/OpenWorm Analysis Toolbox logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/OpenWorm Analysis Toolbox logo.png -------------------------------------------------------------------------------- /documentation/Project History.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Project History.md -------------------------------------------------------------------------------- /documentation/Schafer_validation/Issues with WT2 Analysis Toolbox 1.3.4.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Schafer_validation/Issues with WT2 Analysis Toolbox 1.3.4.md -------------------------------------------------------------------------------- /documentation/Schafer_validation/N2_A_24C_L_5_2015_06_16__19_54_27___feat_comparison.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Schafer_validation/N2_A_24C_L_5_2015_06_16__19_54_27___feat_comparison.pdf -------------------------------------------------------------------------------- /documentation/Schafer_validation/N2_A_24C_R_4_2015_06_16__19_22_48___feat_comparison.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Schafer_validation/N2_A_24C_R_4_2015_06_16__19_22_48___feat_comparison.pdf -------------------------------------------------------------------------------- /documentation/Schafer_validation/Notes on original WT2 Schafer code.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Schafer_validation/Notes on original WT2 Schafer code.md -------------------------------------------------------------------------------- /documentation/Schafer_validation/frame_codes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Schafer_validation/frame_codes.csv -------------------------------------------------------------------------------- /documentation/Worm Tracking Sources and Tools.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/Worm Tracking Sources and Tools.md -------------------------------------------------------------------------------- /documentation/data_examples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/data_examples.md -------------------------------------------------------------------------------- /documentation/database schema/CSV/DataTypes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/CSV/DataTypes.csv -------------------------------------------------------------------------------- /documentation/database schema/CSV/FeatureSpecifications.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/CSV/FeatureSpecifications.csv -------------------------------------------------------------------------------- /documentation/database schema/CSV/FieldDescriptions.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/CSV/FieldDescriptions.csv -------------------------------------------------------------------------------- /documentation/database schema/Features Specifications.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Features Specifications.xlsx -------------------------------------------------------------------------------- /documentation/database schema/Schema - MRC DB.mwb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Schema - MRC DB.mwb -------------------------------------------------------------------------------- /documentation/database schema/Schema - MRC DB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Schema - MRC DB.png -------------------------------------------------------------------------------- /documentation/database schema/Schema - Multi-Worm.erwin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Schema - Multi-Worm.erwin -------------------------------------------------------------------------------- /documentation/database schema/Schema - Multi-Worm.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Schema - Multi-Worm.pdf -------------------------------------------------------------------------------- /documentation/database schema/Schema - Multi-Worm.sql: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/database schema/Schema - Multi-Worm.sql -------------------------------------------------------------------------------- /documentation/dependency_notes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/dependency_notes.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Absolute Coordinates.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Absolute Coordinates.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Feature File Overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Feature File Overview.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Feature Overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Feature Overview.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion - basic tree.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion - basic tree.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion - bends.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion - bends.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion - motion.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion - motion.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion - turns.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion - turns.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion - velocity.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion - velocity.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Locomotion.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Locomotion.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Morphology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Morphology.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Path Figure.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Path Figure.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Path.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Path.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Phenotypic Ontology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Phenotypic Ontology.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Posture.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Posture.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/ReadMe.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/ReadMe.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 1.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 2.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 3.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 3.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 4.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 4.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 5.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 5.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Supplementary Figure 6.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Supplementary Figure 6.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/Ventral Side Annotation and Head Detection.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Ventral Side Annotation and Head Detection.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/Worm Segmentation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/Worm Segmentation.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/body part locations.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/body part locations.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/eigenworms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/eigenworms.png -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 b - bend angle.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 b - bend angle.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 c and d - velocity.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 c and d - velocity.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 e - crawling.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 e - crawling.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 f - motion states.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 f - motion states.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 g - foraging.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 g - foraging.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 h - range.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 h - range.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/fig 4 i - dwelling.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/fig 4 i - dwelling.gif -------------------------------------------------------------------------------- /documentation/feature_descriptions/s1.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s1.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/s2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s2.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/s3.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s3.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/s4.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s4.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/s5.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s5.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/s6.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/s6.md -------------------------------------------------------------------------------- /documentation/feature_descriptions/skeleton_lengths_interpolated.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/feature_descriptions/skeleton_lengths_interpolated.gif -------------------------------------------------------------------------------- /documentation/pypi_notes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/documentation/pypi_notes.md -------------------------------------------------------------------------------- /examples/WCON demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/WCON demo.py -------------------------------------------------------------------------------- /examples/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/__init__.py -------------------------------------------------------------------------------- /examples/feature_subset_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/feature_subset_example.py -------------------------------------------------------------------------------- /examples/generate_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/generate_stats.py -------------------------------------------------------------------------------- /examples/generate_stats_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/generate_stats_plots.py -------------------------------------------------------------------------------- /examples/plot_eigenworms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/plot_eigenworms.py -------------------------------------------------------------------------------- /examples/plot_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/plot_example.py -------------------------------------------------------------------------------- /examples/video_to_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/examples/video_to_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/__init__.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/config.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/events.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/events.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_manipulations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/feature_manipulations.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_metadata/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_metadata/features_list.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/feature_metadata/features_list.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_metadata/features_list_definitions.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/feature_metadata/features_list_definitions.txt -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_metadata/old_features_comparison_notes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/feature_metadata/old_features_comparison_notes.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/feature_processing_options.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/feature_processing_options.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/generic_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/generic_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/locomotion_bends.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/locomotion_bends.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/locomotion_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/locomotion_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/locomotion_turns.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/locomotion_turns.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/master_eigen_worms_N2.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/master_eigen_worms_N2.mat -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/morphology_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/morphology_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/path_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/path_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/posture_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/posture_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/velocity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/velocity.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/features/worm_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/features/worm_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/basic_worm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/basic_worm.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/normalized_worm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/normalized_worm.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/pre_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/pre_features.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/pre_features_helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/pre_features_helpers.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/skeleton_calculator1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/skeleton_calculator1.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/video_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/video_info.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/prefeatures/worm_plotter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/prefeatures/worm_plotter.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/event_features.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/feature_metadata/event_features.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/event_features_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/feature_metadata/event_features_2.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/movement_features.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/feature_metadata/movement_features.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/simple_features.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/feature_metadata/simple_features.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/feature_metadata/simple_features_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/feature_metadata/simple_features_2.csv -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/histogram.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/histogram.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/histogram_manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/histogram_manager.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/pathplot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/pathplot.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/pathplot_manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/pathplot_manager.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/specifications.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/specifications.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/statistics/statistics_manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/statistics/statistics_manager.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/travis_config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/travis_config.txt -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/user_config_example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/user_config_example.txt -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/utils.py -------------------------------------------------------------------------------- /open_worm_analysis_toolbox/version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/open_worm_analysis_toolbox/version.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/setup.py -------------------------------------------------------------------------------- /tests/ReadMe.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/ReadMe.md -------------------------------------------------------------------------------- /tests/test_areas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/test_areas.py -------------------------------------------------------------------------------- /tests/test_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/test_features.py -------------------------------------------------------------------------------- /tests/test_pre_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/test_pre_features.py -------------------------------------------------------------------------------- /tests/test_spec_filtering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/test_spec_filtering.py -------------------------------------------------------------------------------- /tests/unit_test1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/unit_test1.py -------------------------------------------------------------------------------- /tests/validate_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tests/validate_features.py -------------------------------------------------------------------------------- /tools/install-ubuntu-cleanvm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tools/install-ubuntu-cleanvm.sh -------------------------------------------------------------------------------- /tools/test_setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openworm/open-worm-analysis-toolbox/HEAD/tools/test_setup.py --------------------------------------------------------------------------------