Index

A

add_config_argument() (in module wormpose.config.experiment_config) add_resizing_arguments() (in module wormpose.dataset.loaders.resizer)

angle_diff() (in module wormpose.machine_learning.loss) angle_distance() (in module wormpose.pose.distance_metrics)

B

BaseFeaturesDataset (class in wormpose.dataset.base_dataset) BaseFramePreprocessing (class in wormpose.dataset.base_dataset) BaseFramesDataset (class in wormpose.dataset.base_dataset)

BaseResultsExporter (class in wormpose.dataset.base_dataset) BaseScoringDataManager (class in wormpose.images.scoring.scoring_data_manager) BestModels (class in wormpose.machine_learning.best_models_saver)

C

calculate_crop_window_size() (in module wormpose.dataset.features) calculate_max_average_worm_length() (in module wormpose.dataset.features) calculate_similarity() (in module wormpose.images.scoring.image_scoring)

calculate_skeleton() (in module wormpose.pose.centerline) calibrate() (in module wormpose.commands.calibrate_dataset) CenterlineAccuracyCheck (class in wormpose.images.scoring.centerline_accuracy_check) ConstantThreshold (class in wormpose.dataset.image_processing.image_utils)

D

draw_measurements() (in module wormpose.images.worm_drawing)

draw_skeleton() (in module wormpose.images.worm_drawing) draw_width_circle() (in module wormpose.images.worm_drawing)

E

evaluate() (in module wormpose.commands.evaluate_model)

ExperimentConfig (class in wormpose.config.experiment_config) export() (in module wormpose.commands.export_results)

F

features_dataset_resizer() (in module wormpose.dataset.loaders.resizer) FeaturesDataset (class in wormpose.dataset.loaders.tierpsy.features_dataset) fit_bounding_box_to_worm() (in module wormpose.images.scoring.image_scoring)

flip_theta() (in module wormpose.pose.centerline) flip_theta_series() (in module wormpose.pose.centerline) frames_dataset_resizer() (in module wormpose.dataset.loaders.resizer) FramesDataset (class in wormpose.dataset.loaders.tierpsy.frames_dataset)

G

generate() (in module wormpose.commands.generate_training_data) (in module wormpose.machine_learning.eval_data_generator) (wormpose.images.synthetic.synthetic_dataset.SyntheticDataset method) (wormpose.machine_learning.synthetic_data_generator.SyntheticDataGenerator method) GenericFileWriter (class in wormpose.machine_learning.generic_file_writer)

get_dataset_name() (in module wormpose.dataset.loader) get_features() (wormpose.dataset.base_dataset.BaseFeaturesDataset method) (wormpose.dataset.loaders.hdf5features.HDF5Features method) (wormpose.dataset.loaders.tierpsy.features_dataset.FeaturesDataset method) get_features_filename() (in module wormpose.dataset.loaders.tierpsy.features_dataset)

H

HDF5Features (class in wormpose.dataset.loaders.hdf5features)

I

ImagesFolder (class in wormpose.dataset.loaders.images_folder)

interpolate_skeleton() (in module wormpose.pose.centerline)

L

load_config() (in module wormpose.config.experiment_config)

load_eigenworms_matrix() (in module wormpose.pose.eigenworms)

M

make_draw_worm_body() (in module wormpose.images.worm_drawing) modes_to_theta() (in module wormpose.pose.eigenworms) module wormpose.commands.calibrate_dataset wormpose.commands.evaluate_model wormpose.commands.export_results wormpose.commands.generate_training_data wormpose.commands.postprocess_results wormpose.commands.predict_dataset wormpose.commands.train_model wormpose.commands.utils.results_saver wormpose.commands.utils.time_sampling wormpose.commands.visualize_results wormpose.config.default_paths wormpose.config.experiment_config wormpose.dataset.base_dataset wormpose.dataset.features wormpose.dataset.image_processing.frame_preprocessor wormpose.dataset.image_processing.image_utils wormpose.dataset.image_processing.options wormpose.dataset.image_processing.simple_frame_preprocessing wormpose.dataset.loader wormpose.dataset.loaders.hdf5features wormpose.dataset.loaders.images_folder wormpose.dataset.loaders.resizer wormpose.dataset.loaders.sample_data wormpose.dataset.loaders.tierpsy.features_dataset wormpose.dataset.loaders.tierpsy.frames_dataset wormpose.dataset.loaders.tierpsy.results_exporter wormpose.demo.real_simple_visualizer wormpose.demo.synthetic_simple_visualizer wormpose.images.real_dataset wormpose.images.scoring.centerline_accuracy_check wormpose.images.scoring.image_scoring wormpose.images.scoring.results_scoring wormpose.images.scoring.scoring_data_manager wormpose.images.synthetic.synthetic_dataset wormpose.images.worm_drawing wormpose.machine_learning.best_models_saver wormpose.machine_learning.eval_data_generator wormpose.machine_learning.generic_file_writer wormpose.machine_learning.loss wormpose.machine_learning.model wormpose.machine_learning.predict_data_generator wormpose.machine_learning.synthetic_data_generator wormpose.machine_learning.tfrecord_file wormpose.pose.centerline wormpose.pose.distance_metrics wormpose.pose.eigenworms wormpose.pose.headtail_resolution wormpose.pose.postures_model wormpose.pose.results_datatypes wormpose.version

O

on_epoch_end() (wormpose.machine_learning.best_models_saver.BestModels method) open() (wormpose.dataset.base_dataset.BaseFramesDataset method) (wormpose.dataset.loaders.images_folder.ImagesFolder method) (wormpose.dataset.loaders.tierpsy.frames_dataset.FramesDataset method)

OtsuThreshold (class in wormpose.dataset.image_processing.image_utils)

P

post_process() (in module wormpose.commands.postprocess_results) predict() (in module wormpose.commands.predict_dataset)

process() (wormpose.dataset.base_dataset.BaseFramePreprocessing method) (wormpose.dataset.image_processing.simple_frame_preprocessing.SimpleFramePreprocessing method) process_frame() (wormpose.images.real_dataset.RealDataset method)

R

read() (in module wormpose.machine_learning.tfrecord_file) RealDataset (class in wormpose.images.real_dataset) RealSimpleVisualizer (class in wormpose.demo.real_simple_visualizer)

ResizeOptions (class in wormpose.dataset.loaders.resizer) ResultsExporter (class in wormpose.dataset.loaders.tierpsy.results_exporter) run() (in module wormpose.dataset.image_processing.frame_preprocessor)

S

save_config() (in module wormpose.config.experiment_config) ScoringDataManager (class in wormpose.images.scoring.scoring_data_manager) segment_foreground() (in module wormpose.dataset.image_processing.image_utils) SimpleFramePreprocessing (class in wormpose.dataset.image_processing.simple_frame_preprocessing)

skeleton_distance() (in module wormpose.pose.distance_metrics) symmetric_angle_difference() (in module wormpose.machine_learning.loss) SyntheticDataGenerator (class in wormpose.machine_learning.synthetic_data_generator) SyntheticDataset (class in wormpose.images.synthetic.synthetic_dataset) SyntheticSimpleVisualizer (class in wormpose.demo.synthetic_simple_visualizer)

T

TfrecordLabeledDataWriter (class in wormpose.machine_learning.tfrecord_file)

theta_to_modes() (in module wormpose.pose.eigenworms) train() (in module wormpose.commands.train_model)

V

video_names() (wormpose.dataset.base_dataset.BaseFramesDataset method) (wormpose.dataset.loaders.images_folder.ImagesFolder method) (wormpose.dataset.loaders.tierpsy.frames_dataset.FramesDataset method)

visualize() (in module wormpose.commands.visualize_results)

W

wormpose.commands.calibrate_dataset module wormpose.commands.evaluate_model module wormpose.commands.export_results module wormpose.commands.generate_training_data module wormpose.commands.postprocess_results module wormpose.commands.predict_dataset module wormpose.commands.train_model module wormpose.commands.utils.results_saver module wormpose.commands.utils.time_sampling module wormpose.commands.visualize_results module wormpose.config.default_paths module wormpose.config.experiment_config module wormpose.dataset.base_dataset module wormpose.dataset.features module wormpose.dataset.image_processing.frame_preprocessor module wormpose.dataset.image_processing.image_utils module wormpose.dataset.image_processing.options module wormpose.dataset.image_processing.simple_frame_preprocessing module wormpose.dataset.loader module wormpose.dataset.loaders.hdf5features module wormpose.dataset.loaders.images_folder module wormpose.dataset.loaders.resizer module wormpose.dataset.loaders.sample_data module wormpose.dataset.loaders.tierpsy.features_dataset module wormpose.dataset.loaders.tierpsy.frames_dataset module

wormpose.dataset.loaders.tierpsy.results_exporter module wormpose.demo.real_simple_visualizer module wormpose.demo.synthetic_simple_visualizer module wormpose.images.real_dataset module wormpose.images.scoring.centerline_accuracy_check module wormpose.images.scoring.image_scoring module wormpose.images.scoring.results_scoring module wormpose.images.scoring.scoring_data_manager module wormpose.images.synthetic.synthetic_dataset module wormpose.images.worm_drawing module wormpose.machine_learning.best_models_saver module wormpose.machine_learning.eval_data_generator module wormpose.machine_learning.generic_file_writer module wormpose.machine_learning.loss module wormpose.machine_learning.model module wormpose.machine_learning.predict_data_generator module wormpose.machine_learning.synthetic_data_generator module wormpose.machine_learning.tfrecord_file module wormpose.pose.centerline module wormpose.pose.distance_metrics module wormpose.pose.eigenworms module wormpose.pose.headtail_resolution module wormpose.pose.postures_model module wormpose.pose.results_datatypes module wormpose.version module